Branched and linear chimeric compounds, polynucleotides, uses and methods for preparation thereof

ABSTRACT

The present disclosure relates to branched and linear chimeric compounds containing both nucleic acid and non-nucleic acid moieties, as well as to polynucleotides. The present disclosure also relates to uses thereof for stimulating an immune response, and to methods for preparation of the branched chimeric compounds.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/107,291, filed Jan. 23, 2015, which is incorporated herein byreference in its entirety for all purposes.

SUBMISSION OF SEQUENCE LISTING AS ASCII TEXT FILE

The content of the following submission on ASCII text file isincorporated herein by reference in its entirety: a computer readableform (CRF) of the Sequence Listing (file name: 377882005600SEQLIST.txt,date recorded: Jan. 22, 2016, size: 7 KB).

FIELD

The present invention relates to branched and linear chimeric compoundscontaining both nucleic acid and non-nucleic acid moieties, as well asto polynucleotides. The present invention also relates to uses thereoffor stimulating an immune response, and to methods for preparation ofthe branched chimeric compounds.

BACKGROUND

Toll-like receptors (TLRs) are a family of transmembrane proteins thatrecognize conserved microbial molecules, referred to aspathogen-associated molecular patterns, which are distinguishable fromhost molecules. As such TLRs play important roles in innate immuneresponses. TLR3, TLR7, TLR8, TLR9 and TLR13 are nucleic acid sensingTLRs.

Agonists and antagonists of TLRs find use in modulating immuneresponses. TLR agonists are typically employed to stimulate immuneresponses, whereas TLR antagonists are typically employed to inhibitimmune responses (Gosu et al., Molecules, 17:13503-13529, 2012). TLR9,which is expressed by various antigen presenting cells, recognizesunmethylated CpG dinucleotides within nucleic acids. Thuspolynucleotides containing an unmethylated CpG dinucleotide can makeeffective adjuvants through their ability to activate TLR9.Additionally, chimeric compounds containing both a non-nucleic acidmoiety and an unmethylated-CpG containing nucleic acid moiety arecapable of stimulating immune responses.

The potency of a TLR9 agonist is dependent upon the length of thenucleic acid moiety, the residues flanking the unmethylated-CpGdinucleotide, and the efficacy of antigen presenting cell uptake(Marshall et al., Nucleic Acids Research, 31:5122-5133, 2003). Certainbranched chimeric compounds, in which multiple polynucleotides or linearchimeric compounds are attached to a multivalent carrier moiety (e.g., apolysaccharide), have elicited enhanced immune responses relative to theunconjugated polynucleotides or linear chimeric compounds (Marshall etal., supra). A highly branched hydrophilic polysaccharide, marketed asFICOLL® by GE Healthcare, can be used as a multivalent carrier moietyfor branched chimeric compounds. However, traditional linker moietiesused in conjugation of FICOLL® are hydrophobic, which can causeprecipitation of the synthetic intermediates containing FICOLL®. Thisnegatively impacts the processes used to manufacture the branchedchimeric compounds and subsequent ability to store the final products.Moreover, the therapeutic utility of a synthetic TLR agonist isinfluenced by its toxicity.

There remains a need for polynucleotides and chimeric compounds withpotent immunostimulatory activity. Additionally, there remains a needfor potent chimeric compounds that can be reproducibly manufactured.Polynucleotides and chimeric compounds with acceptable toxicity profilesare particularly desirable.

SUMMARY

The present disclosure relates to branched and linear chimeric compoundscontaining both nucleic acid and non-nucleic acid moieties, as well asto polynucleotides. The present disclosure also relates to uses thereoffor stimulating an immune response, and to methods for preparation ofthe branched chimeric compounds.

In one aspect, the present disclosure provides branched chimericcompounds of formula (I): [D-L¹-L²-(PEG)-L³]_(x)-F (I), wherein: D is apolynucleotide or a linear chimeric compound; L¹ is a first linkercomprising an alkylthio group; L² is a second linker comprising asuccinimide group; L³ is a third linker comprising an amide group; PEGis of the formula —(OCH₂CH₂)_(n)—, where n is an integer from 2 to 80; xis an integer from 3 to 300; and F is a branched copolymer of sucroseand epichlorohydrin having a molecular weight of about 100,000 to about700,000 daltons and is connected to L³ via an ether group, wherein thepolynucleotide of D comprises the nucleotide sequence: 5′-TCGGCGCAACGTTC TCGGCGC-3′ (SEQ ID NO:1), wherein the polynucleotide is lessthan 50 nucleotides in length, and wherein one or more linkages betweenthe nucleotides and between the 3′-terminal nucleotide and L¹ arephosphorothioate ester linkages; and wherein the linear chimericcompound of D comprises three nucleic acid moieties and two hexaethyleneglycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides, andwherein one or more linkages between the nucleotides, between thenucleotides and the HEG spacers and between the 3′-terminal nucleotideand L¹ are phosphorothioate ester linkages. In some embodiments, x is20-300, 90-150, or 100-140. In some embodiments, L² is

In some embodiments, L³ is:

In some embodiments, wherein L³ is

In some embodiments, n of the formula —(OCH₂CH₂)_(n)— is 6, 24, 45 or70. In some embodiments, F has a molecular weight of about 300,000 toabout 500,000 daltons. In some embodiments, F is FICOLL® PM 400 (polymermarketed by GE Healthcare). In some embodiments, D is the polynucleotideconsisting of the nucleotide sequence 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQID NO:1). In some embodiments, D is the linear chimeric compoundconsisting of 5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ IDNO:2). In some embodiments, L¹ is —(CH₂)_(m)—S—, wherein m is an integerfrom 2 to 9. In some embodiments, x is from 20 to 200. In someembodiments, x is from 90 to 150, n is 6 and m is 3 or 6. In someembodiments, all of the linkages between the nucleotides, where presentthe linkages between the nucleotides and the HEG spacers, and thelinkage between the 3′-terminal nucleotide and L¹ are phosphorothioateester linkages. The CpG dinucleotides of the polynucleotides or thenucleic acid moieties of the linear chimeric compounds are unmethylated.

In another aspect the present disclosure provides isolatedpolynucleotides comprising the nucleotide sequence 5′-TCGGCGC AACGTTC-3′(SEQ ID NO:3), wherein the polynucleotide is less than 50 nucleotides inlength, and wherein one or more linkages between the nucleotides arephosphorothioate ester linkages. In a related aspect, the presentdisclosure provides isolated polynucleotides comprising the nucleotidesequence 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1), wherein thepolynucleotide is less than 50 nucleotides in length, and one or morelinkages between the nucleotides are phosphorothioate ester linkages. Insome embodiments, the polynucleotide consists of the nucleotide sequenceof 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1). In some embodiments, thepolynucleotide is single-stranded. In some embodiments, thepolynucleotide is a 2′-deoxyribopolynucleotide. In some embodiments, allof the linkages are phosphorothioate ester linkages. The CpGdinucleotides of the polynucleotides are unmethylated.

In a further aspect, the present disclosure provides linear chimericcompounds comprising two nucleic acid moieties and a hexaethylene glycol(HEG) spacer as 5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ (SEQ ID NO:4), whereinthe linear chimeric compound contains fewer than 50 nucleotides, andwherein one or more linkages between the nucleotides and between thenucleotides and the HEG spacer are phosphorothioate ester linkages. In arelated aspect, the present disclosure provides linear chimericcompounds comprising three nucleic acid moieties and two hexaethyleneglycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains fewer than 50 nucleotides, andwherein one or more linkages between the nucleotides and between thenucleotides and the HEG spacers are phosphorothioate ester linkages. Insome embodiments, the linear chimeric compound consists of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2). In someembodiments, the nucleic acid moieties are 2′-deoxyribopolynucleotides.In some embodiments, all of the linkages are phosphorothioate esterlinkages.

Moreover, the present disclosure provides pharmaceutical compositionscomprising (i) a pharmaceutically acceptable excipient, and (ii) one ofthe group consisting of the branched chimeric compound, thepolynucleotide, and the linear chimeric compound of any of the precedingparagraphs of the summary. In some embodiments, the branched chimericcompound, the polynucleotide and the linear chimeric compound are eachcapable of stimulating cytokine production by mammalian leukocytes,comprising one or more of the group consisting of: stimulatingproduction of IFN-alpha by human peripheral blood mononuclear cells;stimulating production of IL-6 by human B lymphocytes; and stimulatingproduction of one or both of IL-12p40 and IL-6 by mouse splenocytes. Insome embodiments, the branched chimeric compound, the polynucleotide andthe linear chimeric compound are each capable of stimulatingproliferation of mammalian B lymphocytes. In some embodiments, thecomposition is a sterile solution. In other embodiments, the compositionis a sterile lyophilized solid. In some embodiments, the compositionfurther comprises an antigen that is not covalently-linked to thebranched chimeric compound, the polynucleotide and the linear chimericcompound present in the composition (e.g., the antigen is mixed withrather than conjugated to the branched chimeric compound, thepolynucleotide or the linear chimeric compound present in thecomposition), branched chimeric compound, the polynucleotide and thelinear chimeric compound present in the composition. In someembodiments, the antigen is a microbial antigen, an allergen or a tumorantigen. In some embodiments, the antigen is an isolated or recombinantprotein. In some embodiments, the composition is essentiallyendotoxin-free.

Additionally the present disclosure provides methods of stimulating animmune response in a mammalian subject, comprising administering to amammalian subject a pharmaceutical composition as described above in anamount sufficient to stimulate an immune response in the mammaliansubject. In some embodiments, stimulating an immune response comprisesone or more of the group consisting of: stimulating IFN-alphaproduction; stimulating IL-6 production; stimulating B lymphocyteproliferation; stimulating interferon pathway-associated geneexpression; stimulating chemoattractant-associated gene expression; andstimulating plasmacytoid dendritic cell (pDC) maturation. In someembodiments, when the pharmaceutical composition further comprises anantigen, stimulating an immune response comprises inducing anantigen-specific antibody response, wherein titer of theantigen-specific antibody response is higher when the antigen isadministered in combination with the branched chimeric compound, thepolynucleotide or the linear chimeric compound than when the antigen isadministered without the branched chimeric compound, the polynucleotideor the linear chimeric compound. In some embodiments, titer of theantigen-specific antibody response is higher when the antigen isadministered in combination with the branched chimeric compound thanwhen the antigen is administered with the corresponding linear chimericcompound.

The present disclosure provides a plurality of methods for using apharmaceutical composition described above in a mammalian subject, suchas a human patient. In one aspect, methods are provided for inducing anantigen-specific antibody response in a mammalian subject, comprisingadministering to a mammalian subject the pharmaceutical composition inan amount sufficient to induce an antigen-specific antibody response inthe mammalian subject. In one aspect, methods are provided forpreventing an infectious disease in a mammalian subject, comprisingadministering to a mammalian subject the pharmaceutical composition inan amount sufficient to prevent an infectious disease in the mammaliansubject. In one aspect, methods are provided for treating or preventingan infectious disease in a mammalian subject, comprising administeringto a mammalian subject the pharmaceutical composition in an amountsufficient to treat or prevent an infectious disease in the mammaliansubject. In one aspect, methods are provided for ameliorating a symptomof an infectious disease in a mammalian subject, comprisingadministering to a mammalian subject the pharmaceutical composition inan amount sufficient to ameliorate a symptom of an infectious disease inthe mammalian subject. In one aspect, methods are provided forameliorating a symptom of an IgE-related disorder in a mammaliansubject, comprising administering to the mammalian subject thepharmaceutical composition in an amount sufficient to ameliorate asymptom of an IgE-related disorder in the mammalian subject. In oneaspect, methods are provided for treating or preventing an IgE-relateddisorder in a mammalian subject, comprising administering to themammalian subject the pharmaceutical composition in an amount sufficientto treat or prevent an IgE-related disorder in the mammalian subject. Inone aspect, methods are provided for a treating cancer in a mammaliansubject, comprising administering to a mammalian subject thepharmaceutical composition in an amount sufficient to treat cancer inthe mammalian subject. In some embodiments, treating cancer comprisesshrinking size of a solid tumor. In some embodiments, treating cancercomprises reducing viable cancer cell numbers. In some embodiments,treating cancer comprises prolonging survival of a cancer patient. Insome embodiments, the cancer is a carcinoma (e.g., head and necksquamous cell carcinoma). In some embodiments, the cancer is a sarcoma.In some embodiments, the cancer is a melanoma. In some embodiments, thecancer is lymphoma.

Moreover the present disclosure provides methods for preparing abranched chimeric compound of formula (I): [D-L¹-L²-(PEG)-L³]_(x)-F (I),wherein: D is a polynucleotide or a linear chimeric compound; L¹ is afirst linker comprising an alkylthio group; L² is a second linkercomprising a succinimide group; L³ is a third linker comprising an amidegroup; PEG is a polyethylene glycol; x is an integer from 3 to 300; andF is a branched copolymer of sucrose and epichlorohydrin having amolecular weight of about 100,000 to about 700,000 daltons and isconnected to L³ via an ether group, wherein the polynucleotide comprisesthe nucleotide sequence: 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1),wherein the polynucleotide is less than 50 nucleotides in length, andwherein one or more linkages between the nucleotides and between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages, andwherein the linear chimeric compound comprises three nucleic acidmoieties and two hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides, andwherein one or more linkages between the nucleotides, between thenucleotides and the HEG spacers and between the 3′-terminal nucleotideand L¹ are phosphorothioate ester linkages, wherein the methodcomprises: reacting a compound of the formula D-L^(1a)-SH, where D is asdefined for formula (I) and L^(1a) is (CH₂)_(m) where m is an integerfrom 2 to 9, with a compound of formula (II): [L^(2a)-(PEG)-L³]_(y)-F(II), wherein L³, PEG and F are as defined for formula (I); L^(2a) is

and y is an integer from 3 to 350. In some embodiments, x is 20-300,90-150, or 100-140; y is 20-350, 30-300, 155-215, or 165-205. In someembodiments, the methods further comprise reacting a compound of theformula D-L^(1a)-SS-L^(1a)-OH with a reducing agent to produce thecompound of the formula D-L^(1a)-SH. In some embodiments, the methodsfurther comprise reacting a compound of the formula (III):[NH₂CH₂CH₂NHC(O)CH₂]_(z)—F (III), wherein F is as defined for formula(I) and z is an integer from 3 to 400, with a compound of the formulaL^(2a)-(PEG)-L^(3a)-Lv, where L^(2a) and PEG are as defined for formula(II); L^(3a) is —NHC(O)CH₂CH₂C(O)— or —C(O)—; and Lv is a leaving group,to form the compound of the formula (II). In some embodiments, z is20-400, 50-300, 190-250, or 200-240. In some embodiments, Lv is(2,5-dioxopyrrolidin-1-yl)oxy. In some embodiments, the methods D is5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2).Variations in the polynucleotide and linear chimeric compound of Dsuitable for use in the methods of the present disclosure are more fullydescribed in the preceding paragraphs.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides a flow chart for the manufacturing scheme used toprepare an exemplary branched chimeric compound, D56-05, (aka[(D56-01)-PEG₆]_(x)-FICOLL).

FIG. 2 illustrates preparation of an exemplary branched chimericcompound, D56-05, (aka [(D56-01)-PEG₆]_(x)-FICOLL).

FIG. 3 shows the reaction scheme for the preparation ofcarboxymethylated-FICOLL.

FIG. 4 shows the reaction scheme for the preparation ofN-(2-aminoethyl)carbamylmethylated-FICOLL.

FIG. 5A-5E show the chemical structures of thesuccinimidyl-((N-maleimidopropionamidol)-polyethyleneglycol) ester andsuccinimidyl-((N-maleimidoalkyl)-polyethyleneglycol) esterheterobifunctional linkers (SM-PEG_(n)).

FIG. 6 shows the reaction scheme for preparation of[maleimide-PEG₆]_(y)-FICOLL.

FIG. 7 provides results from the size exclusion chromatography-highperformance liquid chromatography analysis of[maleimide-PEG₆]_(y)-FICOLL Pilot Lots 4 and 5. A1 is from purifiedPilot Lot 4, A2 is from crude Pilot Lot 4, B1 is from purified Pilot Lot5, and B2 is from crude Pilot Lot 5. Upper and lower chromatograms ineach quadrant represent detection at 215 nm and 260 nm, respectively.[Maleimide-PEG₆]_(y)-FICOLL eluted at about 7.2 min. Unreacted reagentsand small molecules eluted from about 11.2 to 17.3 min.

FIG. 8 shows the reaction scheme for preparation of D56-03 (SEQ ID NO:2)from D56-02 (SEQ ID NO:2), which differ in non-nucleotide moieties attheir 3′ ends.

FIG. 9A-D provide results from the size exclusion chromatography-highperformance liquid chromatography analysis of purified D56-03. FIG. 9Ais from Pilot Lot 4, FIG. 9B is from Pilot Lot 5 Part 1, FIG. 9C is fromPilot Lot 5 Part 2, and FIG. 9D is from Pilot Lot 5 Combined. The D56-03retention time was 12.2 min. TCEP ((tris(2-carboxyethyl)phosphine) wasrun as a control, and eluted as a single peak with a retention time of14.6 min.

FIG. 10 shows the reaction scheme for preparation of D56-05.

FIG. 11A-E show D56-05 nanoparticles, compared with monomeric D56-01,enhance expression of IFN-regulated, chemokine, cytokine, andtransendothelial migration-related genes, leading to enhanced cellrecruitment in injection site muscle. BALB/c mice (n=6/group) wereinjected i.m. with 10 mg D56-05 or D56-01 (CpG-ODN-based doses).Injection site muscle was collected 6 hours following injection toassess IFN-regulated (FIG. 11A), chemokine (FIG. 11B), cytokine (FIG.11C), and transendothelial migration-related (FIG. 11D) gene expression.Gene expression relative to PBS-injected controls was determined by ΔΔCtevaluation (2^(−ΔΔCt)). Data are shown as mean of individual sampleswith 95% CI from a single experiment. (FIG. 11E) Relative proportions ofvarious cell populations in muscle (normalized to total cells) ofD56-05-injected versus D56-01-injected mice (10 mg) at 12-24 hours wereevaluated by flow cytometry. Following light scatter gating andexclusion of lymphocytes (CD3/CD19/CD49b dump channel), cell populationswere identified as follows: macrophages(CD11b⁺/CD11c⁻/F4/80⁺/Ly6C⁺/Ly6G⁻), monocytes(CD11b⁺/CD11c⁻/F4/80⁻/Ly6C⁺/Ly6G⁻), neutrophils (CD11b⁺/CD11c⁻/Ly6G⁺),total CD11b⁺ cells, and cDCs (CD11b⁻/CD11c⁺). Data, shown as means withSEM, are an average of two independent experiments.

FIG. 12A-B show adjuvant effects of D56-05 are dependent on TLR9expression. In FIG. 12A wild-type (C57BL/6) or TLR92/2 mice (n=6) wereinjected i.m. with 10 mg D56-05, and injection site muscle was collected6 hours following injection to determine gene expression. Individualgene fold induction was calculated relative to PBS-injected controls.Data are shown as means with SEM. In FIG. 12B C57BL/6 or TLR92/2 mice(n=8-10) were immunized i.m. with 5 mg rPA in combination with 10 mgD56-05, and. TNA titer levels at day 14 are shown as means. ***p<0.001by Mann-Whitney U test.

FIG. 13A-C show D56-05 nanoparticles enhance IFN-regulated, chemokine,and cytokine genes. BALB/c mice (n=6) were immunized s.c. with 10 mgD56-05 or D56-01. Popliteal lymph nodes were collected 18 hoursfollowing immunization to assess IFN-regulated (FIG. 13A), chemokine(FIG. 13B), and cytokine (FIG. 13C) gene expression. Gene expressionrelative to PBS-injected controls was determined by ΔΔCt evaluation(2^(−ΔΔct)). Data are shown as means of individual samples with 95% CIfrom a single experiment.

FIG. 14 shows D56-05 nanoparticles enhance cell recruitment in draininglymph nodes. The relative proportions of different cell populations inpopliteal lymph nodes of BALB/c mice (n=4-6) immunized s.c. in footpads48 hours earlier with 10 mg D56-05 or D56-01 in combination with 10 or 2mg rPA were analyzed by flow cytometry. Following light scatter gating,cell populations were identified as follows: T cells (CD3⁺/CD19⁻), Bcells (CD3⁻/CD19⁺), NK cells (CD3⁻/CD19⁻/CD49b⁺), and the followingCD3⁻/CD19⁻/CD49b⁻ cell populations: cDCs (CD11b⁻/CD11c⁺/MHC II⁺), pDCs(CD11b⁻/CD11c⁺/MHC II⁺/PDCA1⁺ or B220⁺), mDCs (CD11b⁺/CD11c⁺/MHC II⁺),myeloid cells (CD11b⁺/CD11c⁻/MHC II⁺), macrophages (CD11b⁺/CD11c⁻/MHCII⁺/F4/80⁺/Ly6C⁺/Ly6G⁻), monocytes (CD11b⁺/CD11c⁻/MHCII⁺/F4/80⁻/Ly6C⁺/Ly6G⁻), and neutrophils (CD11b⁺/CD11c⁻/Ly6G⁺). Data areshown as means with SEM and are representative of four independentexperiments.

FIG. 15A-D illustrate that rPA/D56-05 vaccination leads to rapidinduction of anti-rPA Ab response and long-lasting memory in monkeys.Cynomolgus macaques (n=3-6/group) were immunized i.m. (↓) with 10 mg rPAalone or in combination with 1000, 250, or 50 mg D56-05 or 1000 or 250mg D56-01 on days 0 and 28. All monkeys received 25 mg rPA alone (↓) 23wk following initial immunization. TNA and anti-rPA IgG titer levelswere monitored for 25 wk following initial immunization. In FIG. 15A-Btiters 2 wk following initial immunization are shown as the mean with95% CI, and are representative of three independent experiments.*p<0.05, ** p<0.01 by Kruskal-Wallis with Dunn posttest. FIG. 15Cillustrates the correlation between anti-rPA IgG and TNA titer levels 2wk following initial immunization. Spearman rank correlation. FIG. 15Dshows TNA titer data (means) monitored throughout the study.

FIG. 16A-C illustrate that rPA/D56-05 vaccination induces a potentmemory response, mediating complete protection from challenge withaerosolized B. anthracis spores in a monkey prophylactic anthraxchallenge model. Cynomolgus macaques (n=6-8/group) were immunized i.m.(↓) with 10 mg rPA in combination with 1000 or 250 mg D56-05 on day 0and/or 29 (13 or 23). A group (n=6) of nonvaccinated animals was alsoincluded. All monkeys were exposed to a target dose of 200 LD50equivalents of aerosolized B. anthracis spores on day 69, 70, or 71 (↓).In FIG. 16A survival was monitored twice daily for 28 days followingchallenge. In FIG. 16B TNA titer levels were monitored throughout thestudy and for 4 wk following challenge. Data are shown as mean with 95%CI. Cynomolgus macaques (n=4-6) were immunized with 10 mg rPA alone orin combination with 1000, 50, 20, or 5 mg D56-05 on days 0 and 28 (↓).All monkeys received 25 mg rPA alone 10 wk following initialimmunization (↓). In FIG. 16C TNA titer levels were monitored for 12 wkwith titers shown as means.

FIG. 17A-B illustrate that rPA/D56-05 immunization induces greaterprimary and secondary TNA titer responses in mice. Swiss Webster mice(n=25/group) were immunized with 5 mg rPA alone or in combination with 2or 0.5 mg D56-05 or D56-01 on days 0 and 29. TNA titer levels wereassessed (FIG. 17A) 4 wk after the first immunization and (FIG. 17B) 2wk after the second immunization. Data are shown as means with 95% CI.*p<0.05, **p<0.01, ***p<0.001 by Kruskal-Wallis with a Dunn posttest.

FIG. 18 shows that D56-05 nanoparticles are retained at the injectionsite and draining lymph nodes. BALB/c mice (n=5) were injected i.m. with100 mg D56-05 or D56-01. Oligonucleotide content (micrograms per gram oftissue) in injection site muscle, draining lymph nodes (popliteal,inguinal, sciatic, lumbar, and sacral), spleen, liver, and kidney wasassessed at 1 d postinjection. Data are shown with means and arerepresentative of two independent experiments.

FIG. 19 provides a plot showing the body weight over time of miceadministered 1-4 doses (100 μg) of DV56-05 or DV56-01.

FIG. 20 provides a plot showing the tumor size of mice receiving D56-05or D56-30. In brief, about one million E.G-7 OVA cells (ATCC catalognumber CRL-2113) were injected subcutaneously into the flank of C57BL/6mice. Starting on study day 0 (4 days after cell implantation) mice wereinjected intratumorally (i.e., into the established tumor mass) with (50microgram (mcg) of D56-05 or a control non-CpG oligonucleotide (D56-30)in a volume of 150 μL PBS. Injections were administered on Days 0, 3 and7. Mice were observed and tumor size (volume) was measured as indicated.E.G7-OVA is a transgenic cell line, derived from the C57BL/6 (H-2 b)mouse lymphoma cell line EL4, which constitutively secretes chickenovalbumin.

DETAILED DESCRIPTION

The present invention relates to polynucleotides, as well as linear andbranched chimeric compounds containing both nucleic acid and non-nucleicacid moieties. The present invention also relates to uses thereof forstimulating an immune response, and to methods for preparation of thebranched chimeric compounds.

General Methods and Definitions

The practice of the present disclosure will employ, unless otherwiseindicated, conventional techniques of molecular biology, microbiology,cell biology, biochemistry, nucleic acid chemistry, and immunology,which are within the skill of the art. Such techniques are fullydescribed in the literature, see for example: Animal Cell Culture, sixthedition (Freshney, Wiley-Blackwell, 2010); Antibodies, A LaboratoryManual, second edition (Greenfield, ed., Cold Spring HarborPublications, 2013); Bioconjugate Techniques, third edition (Hermanson,Academic Press, 1996); Current Protocols in Cell Biology (Bonifacino etal., ed., John Wiley & Sons, Inc., 1996, including supplements through2014); Current Protocols in Immunology (Coligan et al., eds., John Wiley& Sons, Inc., 1991 including supplements through 2014); CurrentProtocols in Molecular Biology (Ausubel et al., eds., John Wiley & Sons,Inc., 1987, including supplements through 2014); Current Protocols inNucleic Acid Chemistry (Egli et al., ed., John Wiley & Sons, Inc., 2000,including supplements through 2014); Molecular Cloning: A LaboratoryManual, third edition (Sambrook and Russell, Cold Spring HarborLaboratory Press, 2001); Molecular Cloning: A Laboratory Manual, fourthedition (Green and Sambrook, Cold Spring Harbor Laboratory Press, 2012);Oligonucleotide Synthesis: Methods and Applications (Herdewijn, ed.,Humana Press, 2004); Protocols for Oligonucleotides and Analogs,Synthesis and Properties (Agrawal, ed., Humana Press, 1993); and UsingAntibodies: A Laboratory Manual (Harlow and Lane, Cold Spring HarborLaboratory Press, 1998).

As used interchangeably herein, the terms “polynucleotide,”“oligonucleotide” and “nucleic acid” include single-stranded DNA(ssDNA), double-stranded DNA (dsDNA), single-stranded RNA (ssRNA) anddouble-stranded RNA (dsRNA), modified oligonucleotides andoligonucleosides, or combinations thereof. The polynucleotide can belinear, branched, or circularly configured, or the polynucleotide cancontain one or more linear, branched, and/or circular segments.Polynucleotides are polymers of nucleosides joined, generally, throughphosphodiester linkages, although alternate linkages, such asphosphorothioate esters may also be used. A nucleoside consists of apurine (adenine (A) or guanine (G) or derivative thereof) or pyrimidine(thymine (T), cytosine (C) or uracil (U), or derivative thereof) basebonded to a sugar. The four nucleoside units (or bases) in DNA arecalled deoxyadenosine, deoxyguanosine, thymidine, and deoxycytidine. Thefour nucleoside units (or bases) in RNA are called adenosine, guanosine,uridine and cytidine. A nucleotide is a phosphate ester of a nucleoside.

The polynucleotides, linear chimeric compounds and branched chimericcompounds of the present disclosure contain from 14 to 50 nucleotides.In some embodiments, the number of nucleotides is greater than (lowerlimit) 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40 or45. In some embodiments, the number of nucleotides is less than (upperlimit) 51, 50, 45, 40, 35, 30, 25, 24, 23, 22, 21 or 20. That is, thenumber of nucleotides is in the range of about 14 to 50 in which thelower limit is less than the upper limit.

The term “3′” generally refers to a region or position in apolynucleotide 3′ (downstream) from another region or position in thesame polynucleotide.

The term “5′” generally refers to a region or position in apolynucleotide or oligonucleotide 5′ (upstream) from another region orposition in the same polynucleotide or oligonucleotide.

The terms “individual” and “subject” refer to mammals. “Mammals”include, but are not limited to, humans, non-human primates (e.g.,monkeys), farm animals, sport animals, rodents (e.g., mice and rats) andpets (e.g., dogs and cats).

The term “antigen” refers to a substance that is recognized and boundspecifically by an antibody or by a T cell antigen receptor. Antigenscan include peptides, polypeptides, proteins, glycoproteins,polysaccharides, complex carbohydrates, sugars, gangliosides, lipids andphospholipids; portions thereof and combinations thereof. Antigens whenpresent in the compositions of the present disclosure can be syntheticor isolated from nature. Antigens suitable for administration in themethods of the present disclosure include any molecule capable ofeliciting an antigen-specific B cell or T cell response. Haptens areincluded within the scope of “antigen.” A “hapten” is a low molecularweight compound that is not immunogenic by itself but is renderedimmunogenic when conjugated with a generally larger immunogenic molecule(carrier).

“Polypeptide antigens” can include purified native peptides, syntheticpeptides, recombinant peptides, crude peptide extracts, or peptides in apartially purified or unpurified active state (such as peptides that arepart of attenuated or inactivated viruses, microorganisms or cells), orfragments of such peptides. Polypeptide antigens are preferably at leastsix amino acid residues in length.

As used herein, the term “immunogenic” refers to an agent (e.g.,polypeptide antigen) that elicits an adaptive immune response uponadministration under suitable conditions to a mammalian subject. Theimmune response may be B cell (humoral) and/or T cell (cellular)response.

“Adjuvant” refers to a substance which, when mixed with an immunogenicagent such as antigen, nonspecifically enhances or potentiates an immuneresponse to the agent in the recipient upon exposure to the mixture.

The term “agonist” is used in the broadest sense and includes anymolecule that activates signaling through a receptor. For instance, aTLR9 agonist binds a TLR9 receptor and activates a TLR9-signalingpathway.

The term “antagonist” is used in the broadest sense, and includes anymolecule that blocks a biological activity of an agonist. For instance,a TLR9 antagonist blocks a TLR9-signaling pathway.

The terms “immunostimulatory sequence” and “ISS” refer to a nucleic acidsequence that stimulates a measurable immune response (e.g., measured invitro, in vivo, and/or ex vivo). For the purpose of the presentdisclosure, the term ISS refers to a nucleic acid sequence comprising anunmethylated CG dinucleotide. Conversely, the terms “immunoinhibitorysequence” and “IIS” refer to a nucleic acid sequence that inhibits ameasurable immune response (e.g., measured in vitro, in vivo, and/or exvivo). Examples of measurable immune responses include, but are notlimited to, antigen-specific antibody production, cytokine secretion,lymphocyte activation and lymphocyte proliferation.

The terms “CpG” and “CG” are used interchangeably herein to refer to acytosine and guanine separate by a phosphate. These terms refer to alinear sequence as opposed to base-pairing of cytosine and guanine. Thepolynucleotides, linear chimeric compounds and branched chimericcompounds of the present disclosure contain at least one unmethylatedCpG dinucleotide. That is the cytosine in the CpG dinucleotide is notmethylated (i.e., is not 5-methylcytosine).

The terms “antisense” and “antisense sequence” as used herein refer to anon-coding strand of a polynucleotide having a sequence complementary tothe coding strand of mRNA. In preferred embodiments, the polynucleotidesof the present disclosure are not antisense sequences, or RNAi molecules(miRNA and siRNA). That is in preferred embodiments, the polynucleotidesof the present disclosure do not have significant homology (orcomplementarity) to transcripts (or genes) of the mammalian subjects inwhich they will be used. For instance, a polynucleotide of the presentdisclosure for modulating an immune response in a human subject ispreferably less than 80% identical over its length to nucleic acidsequences of the human genome (e.g., a polynucleotide that is 50nucleotides in length would share no more than 40 of the 50 bases with ahuman transcript). That is, in preferred embodiments, thepolynucleotides are less than 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%,40%, 35%, 30%, 25% or 20%, identical to nucleic acid sequences ofmammalian subjects (e.g., such as humans, nonhuman primates, farmanimals, dogs, cats, rabbits, rats, mice, etc.) in which they are to beused.

“Stimulation” of a response or parameter includes eliciting and/orenhancing that response or parameter when compared to otherwise sameconditions except for a parameter of interest, or alternatively, ascompared to another condition (e.g., increase in TLR-signaling in thepresence of a TLR agonist as compared to the absence of the TLRagonist). For example, “stimulation” of an immune response means anincrease in the response.

“Inhibition” of a response or parameter includes blocking and/orsuppressing that response or parameter when compared to otherwise sameconditions except for a parameter of interest, or alternatively, ascompared to another condition (e.g., decrease in TLR-signaling in thepresence of a TLR agonist and a TLR antagonist as compared to thepresence of the TLR agonist in the absence of the TLR antagonist). Forexample, “inhibition” of an immune response means a decrease in theresponse.

An “effective amount” of an agent disclosed herein is an amountsufficient to carry out a specifically stated purpose. An “effectiveamount” may be determined empirically and in a routine manner, inrelation to the stated purpose. An “effective amount” or an “amountsufficient” of an agent is that amount adequate to effect a desiredbiological effect, such as a beneficial result, including a beneficialclinical result. The term “therapeutically effective amount” refers toan amount of an agent (e.g., TLR inhibitor) effective to “treat” adisease or disorder in a subject (e.g., a mammal such as a human). Inthe case of allergy, a therapeutically effective amount of the agentreduces a sign or symptom of the allergy.

The terms “treating” or “treatment” of a disease refer to executing aprotocol, which may include administering one or more drugs to anindividual (human or otherwise), in an effort to alleviate signs orsymptoms of the disease. Thus, “treating” or “treatment” does notrequire complete alleviation of signs or symptoms, does not require acure, and specifically includes protocols that have only a palliativeeffect on the individual. As used herein, and as well-understood in theart, “treatment” is an approach for obtaining beneficial or desiredresults, including clinical results. Beneficial or desired clinicalresults include, but are not limited to, alleviation or amelioration ofone or more symptoms, diminishment of extent of disease, stabilized(i.e., not worsening) state of disease, preventing spread of disease,delay or slowing of disease progression, amelioration or palliation ofthe disease state, and remission (whether partial or total), whetherdetectable or undetectable. “Treatment” can also mean prolongingsurvival as compared to expected survival of an individual not receivingtreatment.

“Palliating” a disease or disorder means that the extent and/orundesirable clinical manifestations of the disease or disorder arelessened and/or time course of progression of the disease or disorder isslowed, as compared to the expected untreated outcomel. Especially inthe allergy context, palliation may occur upon stimulation of a Th1immune response against an allergen(s). Further, palliation does notnecessarily occur by administration of one dose, but often occurs uponadministration of a series of doses. Thus, an amount sufficient topalliate a response or disorder may be administered in one or moredoses.

As used herein and in the appended claims, the singular forms “a,” “an”and “the” include plural referents unless otherwise indicated or clearfrom context. For example, “a polynucleotide” includes one or morepolynucleotides.

Reference to “about” a value or parameter describes variations of thatvalue or parameter. For example, description referring a molecularweight of about 400,000 daltons encompasses molecular weights of 360,000to 440,000 daltons.

It is understood that aspects and embodiments described herein as“comprising” include “consisting of” and “consisting essentially of”embodiments.

I. Polynucleotides and Chimeric Compounds

The present disclosure provides polynucleotides, linear chimericcompounds and branched chimeric compounds useful, inter alia, formodulating an immune response in a mammalian subject, such as a humanpatient. The present disclosure is based, in part, on the discovery thatsome chimeric compounds containing nucleic acid moieties covalentlybound to non-nucleic acid spacer moieties and/or a polymeric carrierhave immunomodulatory activity (particularly in human cells), includingin cases in which the nucleic acid moieties have a sequence that, ifpresented as an isolated polynucleotide, do not exhibit appreciableimmunomodulatory activity (e.g., inferior or unmeasurable activity). Insome embodiments, the immunomodulatory activity comprisingimmunostimulatory activity. In other embodiments, the immunomodulatoryactivity comprising immunoinhibitory activity.

A. Polynucleotides

In one aspect, polynucleotides comprising an unmethylated CpGdinucleotide are provided. The polynucleotides are capable ofstimulating an immune response or constitute chimeric compounds forstimulating an immune response. In some embodiments, provided is apolynucleotide comprising the nucleotide sequence 5′-TCGGCGC AACGTTC-3′(SEQ ID NO:3). In some embodiments, provided is a polynucleotidecomprising the nucleotide sequence 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ IDNO:1). In some embodiments, the polynucleotide is less than 50nucleotides in length (i.e., the polynucleotide contains less than 50nucleotides). In some embodiments, one or more linkages between thenucleotides are phosphorothioate ester linkages. In some embodiments,one or more linkages between the nucleotides are phosphodiesterlinkages. In preferred embodiments, 5′-TCGGCGC AACGTTC-3′ (SEQ ID NO:3)or 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1) is located at the5′-terminus of the polynucleotide (i.e., any additional nucleotides areadded to the 3′-terminus). In some embodiments, the polynucleotideconsists of the nucleotide sequence of 5′-TCGGCGC AACGTTC TCGGCGC-3′(SEQ ID NO:1). In some embodiments, the polynucleotide issingle-stranded. In some embodiments, the polynucleotide is a2′-deoxyribopolynucleotide. In some embodiments, all of the linkagesbetween the nucleotides are phosphorothioate ester linkages.

B. Linear Chimeric Compounds

In another aspect, linear chimeric compounds comprising a nucleic acidmoiety comprising an unmethylated CpG dinucleotide are provided. Thelinear chimeric compounds are capable of stimulating an immune responseor constitute branched chimeric compounds for stimulating an immuneresponse. In some embodiments, provided is a linear chimeric compoundcomprising nucleic acid moieties and non-nucleic acid spacer moieties.In some embodiments, the linear chimeric compound comprises a corestructure with the formula N₁-Sp₁-N₂ or N₁-Sp₁-N₂-Sp₂-N₃ (wherein N₁,N₂, and N₃ are nucleic acid moieties, Sp₁ and Sp₂ are non-nucleic acidspacer moieties, and Sp₁ and Sp₂ are covalently bound to exactly twonucleic acid moieties). In some of these embodiments, the linearchimeric compound comprises a core structure of the formula(5′-N₁-3′)-Sp₁-(5′-N₂-3′). In some of these embodiments, the linearchimeric compound comprises a core structure of the formula(5′-N₁-3′)-Sp₁-(5′-N₂-3′)-Sp₂-(5′-N₃-3′). In some embodiments, thespacer moieties are a hexaethylene glycol (HEG). In some embodiments,the linear chimeric compound contains less than 50 nucleotides (i.e.,sum of N₁, N₂, and optionally N₃ is less than 50). In some embodiments,each nucleic acid moiety N is less than 8 nucleotides in length,preferably 7 nucleotides in length.

In some embodiments, provided is linear chimeric compound comprising twonucleic acid moieties and a hexaethylene glycol spacer as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ (SEQ ID NO:4), wherein the linearchimeric compound contains less than 50 nucleotides (i.e., sum of N₁ andN₂ is less than 50), and wherein one or more linkages between thenucleotides and between the nucleotides and the HEG spacer arephosphorothioate ester linkages. In some embodiments, provided is alinear chimeric compound comprising three nucleic acid moieties and twohexaethylene glycol spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides (i.e.,sum of N₁, N₂, and N₃ is less than 50), and wherein one or more linkagesbetween the nucleotides and between the nucleotides and the HEG spacersare phosphorothioate ester linkages. In some embodiments,5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ (SEQ ID NO:4) or5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2) islocated at the 5′-terminus of the linear chimeric compound (i.e., anyadditional nucleotides are added to the 3′-terminus). In someembodiments, provided is a linear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2). In someembodiments, one or more linkages between the nucleotides arephosphodiester linkages. In some embodiments, all of the internucleotidelinkages and the linkages between nucleotides and the HEG spacers arephosphorothioate ester linkages. In some embodiments, the nucleic acidmoieties of the linear chimeric compound are a2′-deoxyribopolynucleotides. The CpG dinucleotides of the nucleic acidmoieties of the linear chimeric compounds are unmethylated.

The present disclosure further provides linear chimeric compoundscomprising one of the group consisting of:

(SEQ ID NO: 9) 5′-TCGTTCG-3′-HEG-5′-TCGTTCG-3′-HEG-5′-AACGTTC-3′(D56-16), (SEQ ID NO: 10)5′-TCGTTCG-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGTTCG-3′ (D56-17),(SEQ ID NO: 11) 5′-TCGGCGC-3′-HEG-5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′(D56-18), (SEQ ID NO: 12)5′-TCGCCGG-3′-HEG-5′-TCGCCGG-3′-HEG-5′-AACGTTC-3′ (D56-19),(SEQ ID NO: 13) 5′-TCGCCGG-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGCCGG-3′(D56-20), (SEQ ID NO: 14)5′-TCGATCG-3′-HEG-5′-TCGATCG-3′-HEG-5′-AACGTTC-3′ (D56-21),(SEQ ID NO: 15) 5′-TCGTCGT-3′-HEG-5′-TCGTCGT-3′-HEG-5′-AACGTTC-3′(D56-22), and (SEQ ID NO: 16)5′-TCGTCGT-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGTCGT-3′ (D56-23).In some of these embodiments, the linear chimeric compound contains lessthan 50 nucleotides, and 5′-TCG-3′ of the nucleotide sequence is locatedat the 5′-terminus of the linear chimeric compound (i.e., any additionalnucleotides are added to the 3′-terminus). In some embodiments, one ormore linkages between the nucleotides and between the nucleotides andthe HEG spacers are phosphorothioate ester linkages. In someembodiments, one or more linkages between the nucleotides arephosphodiester linkages. In some embodiments, all of the internucleotidelinkages and the linkages between nucleotides and the HEG spacers arephosphorothioate ester linkages. In some embodiments, the nucleic acidmoieties of the linear chimeric compound are a2′-deoxyribopolynucleotides. The CpG dinucleotides of the nucleic acidmoieties of the linear chimeric compounds are unmethylated.

C. Branched Chimeric Compounds

The branched chimeric compounds of the present disclosure comprise apolynucleotide or a linear chimeric compound that is covalently linkedto a branched copolymer of sucrose and epichlorohydrin via apolyethylene glycol. The maleimide-activated FICOLL intermediate of thebranched chimeric compounds of the present disclosure containing apolyethylene glycol have improved solubility and stability as comparedto the intermediates of the previously disclosed branched chimericcompounds. Thus, the branched chimeric compounds of the presentdisclosure have improved manufacturability and storability as comparedto the branched chimeric compounds C-137 and C-138 of U.S. Pat. Nos.8,597,665, 8,114,418, and 7,785,610 of Dynavax Technologies Corporation.The branched chimeric compounds of the present disclosure also possesspotent immunomodulatory activity (e.g., immunostimulatory orimmunoinhibitory activity) and low toxicity in vitro and in vivo.

In some embodiments, this disclosure provides a branched chimericcompound of formula (I):

[D-L¹-L²-(PEG)-L³]_(x)-F  (I)

wherein:

D is a polynucleotide or a linear chimeric compound;

L¹ is a first linker comprising an alkylthio group;

L² is a second linker comprising a succinimide group;

L³ is a third linker comprising an amide group;

PEG is a polyethylene glycol;

x is an integer from 3 to 300; and

F is a branched copolymer of sucrose and epichlorohydrin.

The branched chimeric compound of formula (I) comprises three or morepolynucleotides or linear chimeric compounds D linked to a multivalentmoiety F via a polyethylene glycol (PEG) and various linkers L¹, L² andL³. The polynucleotide or nucleic acid moiety of the linear chimericcompound of D comprises an unmethylated CpG dinucleotide.

In some embodiments, D is a polynucleotide comprising the nucleotidesequence 5′-TCGGCGC-3′. In some embodiments, D is a polynucleotidecomprising the nucleotide sequence 5′-TCGGCGC AACGTTC-3′ (SEQ ID NO:3).In some embodiments, D is a polynucleotide comprising the nucleotidesequence 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1). In someembodiments, the polynucleotide of D is less than 50 nucleotides inlength (i.e., the polynucleotide of D contains less than 50nucleotides). In some embodiments, one or more linkages between thenucleotides and between the 3′-terminal nucleotide of D and L¹ arephosphorothioate ester linkages. In some embodiments, 5′-TCGGCGCAACGTTC-3′ (SEQ ID NO:3) or 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1)of D is located at the 5′ terminus of the polynucleotide (i.e., anyadditional nucleotides are added to the 3′-terminus). In someembodiments, D is a polynucleotide consisting of the nucleotide sequenceof 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1). In some embodiments, thepolynucleotide of D is single-stranded. In some embodiments, thepolynucleotide of D is a 2′-deoxyribopolynucleotide. In someembodiments, one or more linkages between the nucleotides arephosphodiester linkages. In some embodiments, all of the linkagesbetween the nucleotides and the linkage between the 3′-terminalnucleotide of D and L¹ are phosphorothioate ester linkages. The CpGdinucleotides of the polynucleotide of D are unmethylated.

In some embodiments, D is a linear chimeric compound comprising nucleicacid moieties and non-nucleic acid spacer moieties. In some embodiments,the linear chimeric compound comprises a core structure with the formulaN₁-Sp₁-N₂ or N₁-Sp₁-N₂-Sp₂-N₃ (wherein N₁, N₂, and N₃ are nucleic acidmoieties, Sp₁ and Sp₂ are non-nucleic acid spacer moieties, and Sp₁ andSp₂ are covalently bound to exactly two nucleic acid moieties). In someof these embodiments, the linear chimeric compound comprises a corestructure of the formula (5′-N₁-3′)-Sp₁-(5′-N₂-3′). In some of theseembodiments, the linear chimeric compound comprises a core structure ofthe formula (5′-N₁-3′)-Sp₁-(5′-N₂-3′)-Sp₂-(5′-N₃-3′). In someembodiments, N₁ has the sequence 5′-TCGGCGC-3′. In some embodiments, N₂has the sequence 5′-AACGTTC-3′. In some embodiments, N₃ has the sequence5′-TCGGCGC-3′. In some embodiments, N₁ has the sequence 5′-TCGGCGC-3′and N₂ has the sequence 5′-AACGTTC-3′. In some embodiments, N₁ has thesequence 5′-TCGGCGC-3′, N₂ has the sequence 5′-AACGTTC-3′, and N₃ hasthe sequence 5′-TCGGCGC-3′. In some of these embodiments, the spacermoieties are hexaethylene glycol (HEG). In some embodiments, Sp₁ ishexaethylene glycol (HEG). In some embodiments, Sp₂ is hexaethyleneglycol (HEG). In some embodiments, the linear chimeric compound of Dcontains less than 50 nucleotides (i.e., sum of N₁, N₂, and optionallyN₃ is less than 50). In some embodiments, 5′-TCGGCGC-3′ is located atthe 5′-terminus of the linear chimeric compound (i.e., any additionalnucleotides are added to the 3′-terminus). In some embodiments, eachnucleic acid moiety N is less than 8 nucleotides in length, preferably 7nucleotides in length. In some embodiments, each nucleic acid moiety Nis from 4 to 7, preferably 5 to 7, or 6 or 7 nucleotides in length. TheCpG dinucleotides of the nucleic acid moieties of the linear chimericcompound of D are unmethylated.

In some embodiments, D is linear chimeric compound comprising twonucleic acid moieties and a hexaethylene glycol spacer as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ (SEQ ID NO:4), wherein the linearchimeric compound contains less than 50 nucleotides (i.e., sum of N₁ andN₂ is less than 50), and wherein one or more linkages between thenucleotides, between the nucleotides and the HEG, and between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages. Insome embodiments, D is a linear chimeric compound comprising threenucleic acid moieties and two hexaethylene glycol spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides (i.e.,sum of N₁, N₂, and N₃ is less than 50), and wherein one or more linkagesbetween the nucleotides and between the nucleotides and the HEG spacerare phosphorothioate ester linkages. In some embodiments,5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ (SEQ ID NO:4) or5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2) of D islocated at the 5′ terminus of the linear chimeric compound (i.e., anyadditional nucleotides are added to the 3′-terminus). In someembodiments, D is linear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2). In someembodiments, one or more linkages between the nucleotides arephosphodiester linkages. In some embodiments, all of the internucleotidelinkages, the linkages between nucleotides and the HEG spacers, and thelinkage between the 3′-terminal nucleotide and L¹ in the linear chimericcompound of D are phosphorothioate ester linkages. In some embodiments,the nucleic acid moieties of the linear chimeric compound of D are2′-deoxyribopolynucleotides. The CpG dinucleotides of the nucleic acidmoieties of the linear chimeric compound of D are unmethylated.

Polysaccharides derivatized to allow linking to nucleic acid moietiescan be used as a multivalent carrier moiety serving as the branchingunit for the branched chimeric compounds of the present disclosure.Suitable polysaccharides may be naturally occurring polysaccharides orsynthetic polysaccharides. Exemplary polysaccharides include, e.g.,dextran, mannin, chitosan, agarose, and starch. Mannin may be used, forexample, because there are mannin (mannose) receptors on immunologicallyrelevant cell types, such as monocytes and alveolar macrophages, and sothe polysaccharide spacer moiety may be used for targeting particularcell types. In some embodiments, the polysaccharide is cross-linked. Apreferred multivalent carrier moiety is epichlorohydrin-crosslinkedsucrose (e.g., branched copolymer of sucrose and epichlorohydrin brandedas FICOLL® by GE Healthcare).

In some embodiments F of formula (I) is a branched copolymer of sucroseand epichlorohydrin having a molecular weight of about 100,000 to about700,000 daltons, which is connected to L³ via an ether group. The ethergroup is derived from a sucrose hydroxyl of the copolymer. In someembodiments, F is a branched copolymer of sucrose and epichlorohydrinhaving a molecular weight greater than (lower limit) about 100,000,200,000, 300,000, 400,000, 500,000 or 600,000 daltons. In someembodiments, F is a branched copolymer of sucrose and epichlorohydrinhaving a molecular weight less than (upper limit) about 700,000,600,000, 500,000, 400,000, 300,000, or 200,000 daltons. That is themolecular weight of F can be any of a range of sizes from about 100,000to about 700,000 daltons in which the lower limit is less than the upperlimit. In some embodiments, F has a molecular weight of from about300,00 to 500,00 daltons (e.g., FICOLL® PM 400 of GE Healthcare).

It is intended and understood that each and every variation of Fdetailed herein for the branched chimeric compound of formula (I) can becombined with each and every variation of D detailed herein for thebranched chimeric compound of formula (I) as if each and everycombination is individually described. For example, in some embodiments,provided is a branched chimeric compound of the formula (I):

[D-L¹-L²-(PEG)-L³]_(x)-F  (I),

wherein:

D is a polynucleotide or a linear chimeric compound;

L¹ is a first linker comprising an alkylthio group;

L² is a second linker comprising a succinimide group;

L³ is a third linker comprising an amide group;

PEG is a polyethylene glycol (e.g., —(OCH₂CH₂)_(n)—, where n is aninteger from 2 to 80);

x is an integer from 3 to 300; and

F is a branched copolymer of sucrose and epichlorohydrin having amolecular weight of about 100,000 to about 700,000 daltons and isconnected to L³ via an ether group,

wherein the polynucleotide comprises the nucleotide sequence: 5′-TCGGCGCAACGTTC TCGGCGC-3′ (SEQ ID NO:1), wherein the polynucleotide of D isless than 50 nucleotides in length, and wherein one or more linkagesbetween the nucleotides are phosphorothioate ester linkages, andwherein the linear chimeric compound of D comprises three nucleic acidmoieties and two hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinone or more linkages between the nucleotides, between the nucleotidesand the HEG spacers and between the 3′-nucleotide and L¹ arephosphorothioate ester linkages.

The present disclosure provides a branched chimeric compound of formula(I) comprising a polynucleotide or a liner chimeric compound D linked toa multivalent moiety F via a polyethylene glycol (PEG) and variouslinkers L¹, L² and L³ as: -L¹-L²-(PEG)-L³-, wherein L¹ is a first linkercomprising an alkylthio group; L² is a second linker comprising asuccinimide group; L³ is a third linker comprising an amide group; andPEG is —(OCH₂CH₂)_(n)—.

Polyethylene glycol has found wide use in conjugating/modifyingbiologically active molecules because it is nontoxic, nonimmunogenic,hydrophilic, water soluble and highly flexible. The PEG containingmoiety unit of the chimeric compounds of this disclosure provides bettersolubility and stability for these compounds compared to conjugates thatemploy hydrophobic moieties such as the methylcyclohexyl (MC) moietiescommonly used in bio-conjugation. The number of ethylene glycol units inthe PEG linker can be tailored so as to optimize the length,hydrophilicity, and particle size of the branched chimeric compound.

In some embodiments, the PEG of formula (I) is of the formula—(OCH₂CH₂)_(n)—, where n is an integer from 2 to 80. In someembodiments, n is an integer greater than (lower limit) 2, 4, 6, 8, 10,12, 14, 16, 18 or 20. In some embodiments, n is an integer less than(upper limit) 80, 70, 60, 50 or 40. That is, n can be an integer in therange of from about 2 to 80 in which the lower limit is less than theupper limit. In some embodiments, n is 2, 4, 6, 24, 45, 48 or 70. Insome embodiments, n is 6, 24, 45 or 70. In some embodiments, n is 2, 4,6, 24, 28, 45, 48 or 70. In some embodiments, n is 6, 24, 28, 45 or 70.In a preferred embodiment, PEG is —(OCH₂CH₂)₆—.

The PEG in the branched chimeric compounds of the present disclosure, isattached at one end to a 3′-nucleotide of the polynucleotide or thelinear chimeric compound of D via linkers comprising a succinimide groupand is attached at the other end to the multivalent moiety F via alinker comprising an amide group. An alkylthio group is employed tofacilitate the chemical coupling between the 3′-nucleotide of thepolynucleotide or the linear chimeric compound of D and the succinimidegroup. Thus, the first linker L¹ is a linker comprising an alkylthiogroup, which is capable of linking a 3′-terminal phosphate moiety of anucleic acid to a succinimide group of the second linker L² by way of aterminal sulfhydryl group (—SH) of a precursor comprising L¹ reactingwith a maleimide group in a precursor comprising L² to form the athiosuccinimdo linkage between L¹ and L². In some embodiments, L¹ is ofthe formula -L^(1a)-S—, where L^(1a) is an alkylene group, for example,a group of formula (CH₂)_(m) where m is an integer from 2 to 9. In someembodiments, L¹ is an alkylthio group of the formula —(CH₂)_(m)S—, wherem is an integer from 2 to 9. In some of the embodiments, m is 2, 3, 4,5, 6, 7, 8 or 9. In some embodiments, m is from 3 to 6. In someembodiments, m is 3 or 6. In a preferred embodiment, m is 6. In anotherpreferred embodiment, m is 3. In some embodiments, L¹ is —(CH₂)₆S— or—(CH₂)₃S—.

The second linker L² is a linker comprising a succinimide group. In someembodiments, L² further comprises an alkyl spacer group (e.g.,—CH₂CH₂—), and/or an alkyl amide spacer group (e.g., —CH₂CH₂C(O)NH—). Insome embodiments, L² is

In some embodiments, L² is

In some embodiments, L² is of the formula

wherein L^(2b) is an alkyl spacer group (e.g., —CH₂CH₂— or—CH₂CH₂CH₂CH₂—), and/or an alkyl amide spacer group (e.g.,—CH₂CH₂C(O)NH—). In some embodiments, L^(2b) is —CH₂CH₂C(O)NHCH₂CH₂—. Insome embodiments, L^(2b) is —CH₂CH₂C(O)NHCH₂CH₂CH₂—.

In some embodiments, the -L¹-L²- moiety is

The third linker L³ is a linker comprising an amide group, whichcovalently links the PEG via an ether group to the multivalent moiety F.In some embodiments, L³ further comprises one or more alkyl spacergroups (e.g., —CH₂CH₂—), one or more amide spacer groups (e.g., —C(O)NH—or —NHC(O)—), or a combination thereof. In some embodiments, L³ is ofthe formula

wherein L^(3a) is a spacer capable of linking an alkyl group and anamine, such as a spacer of the formula —NHC(O)CH₂CH₂C(O)—, —OC(O)— or—C(O)—. The (2-aminoethyl)aminocarbonylmethyl moiety of L³ may beattached to F by reacting hydroxyl groups on F with chloroacetate andthen coupling with ethylene diamine.

In some embodiments, L³ is

It is intended and understood that each and every variation of L¹, L²,L³ and PEG detailed herein for the branched chimeric compound of formula(I) may be combined with each other, and may be combined further witheach and every variation of D and F detailed herein for the branchedchimeric compound of formula (I), as if each and every combination isindividually described. For example, in some embodiments, the-L²-(PEG)-L³- moiety is of the formula (A), (B), (C), (D), (E), (F) or(G):

In some embodiments, the -L¹-L²-(PEG)-L³- moiety is

In some embodiments, the branched chimeric compound is of the formula

wherein D is linear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2) whereinone or more linkages between the nucleotides, between the nucleotidesand the HEG spacers and between the 3′-terminal nucleotide and L¹ arephosphorothioate ester linkages, F is a branched copolymer of sucroseand epichlorohydrin having a molecular weight of about 400,000, n is 6,24, 45 or 70, and x is an integer from 3 to 300, wherein F is connectedto the methylene group via an ether linkage. In some embodiments, n is 6and x is from 90 to 150.

In some embodiments, the branched chimeric compound is of the formula

wherein D is linear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2) whereinone or more linkages between the nucleotides, between the nucleotidesand the HEG spacers and between the 3′-terminal nucleotide and L¹ arephosphorothioate ester linkages, F is a branched copolymer of sucroseand epichlorohydrin having a molecular weight of about 400,000, n is 6,24, 45 or 70, and x is an integer from 3 to 300, wherein F is connectedto the methylene group via an ether linkage. In some embodiments, n is 6and x is from 90 to 150. In some embodiments, n is 45 and x is from 90to 150.

The number of polynucleotides or linear chimeric compounds of D in thebranched chimeric compound of formula (I) can range from 3 to about 300.That is, x is an integer from 3 to 300. In some embodiments, x is aninteger greater than (lower limit) 3, 6, 9, 12, 20, 30, 40, 50, 60, 70,80, 90, 100, 110, 120, 130, 140, 150, 155, 165, 190 or 200. In someembodiments, x is an integer less than (upper limit) 300, 275, 250, 225,215, 210, 205, 200, 190, 180, 160, 150, 140, 130, 120, 110, 100, 90, 80,70, 60 or 50. That x can be an integer in the range of from about 3 to300 in which the lower limit is less than the upper limit. For instancein some embodiments, x is from 20 to 300, from 20 to 200, from 60 to180, from 90 to 150, from 100 to 140, or from 110 to 130. In someembodiments, x is about 120±30. In a preferred embodiment, x is about120.

Typical preparations of chimeric compounds of the disclosure are aheterogeneous mixture composed of chimeric compounds having adistribution of loading ratio with a specified average molecular weightor approximate number of D moieties per multivalent carrier moiety F,although reagents and reaction conditions may be controlled to achievereproducibly desired loading ratio. In one aspect, a composition isprovided comprising one or more branched chimeric compounds of formula(I) or variations thereof described herein. In some embodiments, thecomposition comprises a plurality of branched chimeric compounds ofdefined loading ratio and average molecular weight. In some embodiments,the composition comprises a heterogeneous mixture of compounds offormula (I), wherein D, PEG, L¹, L², L³, F and x are independently asdescribed herein for formula (I), wherein the F moieties of the chimericcompounds of the mixture have an average molecular weight between about200,000 and about 600,000 Daltons, and wherein the chimeric compounds ofthe mixture have an average loading ratio (x) between about 60 and about180.

In some embodiments, the composition comprises a heterogeneous mixtureof compounds of formula (I), wherein D, PEG, L¹, L², L³, F and x areindependently as described herein for formula (I), wherein the Fmoieties of the chimeric compounds of the mixture having an averagemolecular weight between about 300,000 and about 500,000 (e.g., about400,000) in Daltons. In some embodiments, the F moieties of the chimericcompounds of the mixture have a molecular weight between about400,000±100,000 Daltons. In some embodiments, the composition comprisesa heterogeneous mixture of compounds of formula (I), wherein D, PEG, L¹,L², L³, F and x are independently as described herein for formula (I),wherein the chimeric compounds of the mixture having an average loadingratio (x) between about 90 and about 150 or between about 100 and about140 (e.g., about 120). In some embodiments, the chimeric compounds ofthe mixture have a loading ratio (x) of about 120±30 or about 120±20).In some embodiments, the composition comprises a heterogeneous mixtureof branched chimeric compounds of formula (I), wherein D, PEG, L¹, L²,L³, F and x are independently as described herein for formula (I),wherein the F moieties of the branched chimeric compounds of the mixturehave a molecular weight of about 400,000±100,000 daltons, and whereinthe branched chimeric compounds of the mixture have an average loadingratio of about 120±30).

The polynucleotides, linear chimeric compounds and branched chimericcompounds of the present disclosure have appreciable immunomodulatoryactivity (e.g., at least 3-fold higher than a non-immunomodulatorycontrol). In some embodiments, the immunomodulatory activity comprisesimmunostimulatory activity. In other embodiments, the immunomodulatoryactivity comprises immunoinhibitory activity. The polynucleotides may besingle stranded or double stranded. The polynucleotides may be RNA, DNAor a RNA/DNA hybrid. The internucleotide linkages, the linkages betweennucleotides and the HEG spacers, and the linkage between the 3′-terminalnucleotide and the linker L¹ may be phosphate or thiophosphate esters.

In some embodiments, the polynucleotides, linear chimeric compounds andbranched chimeric compounds of the present disclosure possessimmunostimulatory activity. In these embodiments, D comprises SEQ IDNO:1, SEQ ID NO:2, SEQ ID NO:3 or SEQ ID NO:4. In some embodiments, Dcomprises one of the group consisting of SEQ ID NOS:9-16. The CpGdinucleotides of the polynucleotides or nucleic acid moieties of D areunmethylated. In some embodiments, 5′-TCG-3′ of the polynucleotides ornucleic acid moieties of D are located at the 5′-terminus (e.g., anyadditional nucleotides are added to the 3′-terminus). In preferredembodiments, the polynucleotide does not comprise a Toll-like receptor(TLR) inhibitory motif. In preferred embodiments, the polynucleotides donot comprise TLR7, TLR8 and/or TLR9 inhibitory motifs. Exemplary TLR7inhibitory motifs include 5′-Q_(z′)TGC-3′, 5′-Q_(z′)UGC-3′,5′-Q_(z′)TIC-3′, and 5′-Q_(z′)TTC-3′, wherein Q is a nucleotide ornucleotide analog, and z′ is 0, 1 or 2. That is Qz, is at the 5′-end ofthe polynucleotide. An exemplary TLR8 inhibitory motif is5′-X₁X₂X₃-M_(y′)-3′, wherein X₁ is A, T or C, X₂ is G or I, X₃ is I orA, M is a nucleotide or nucleotide analog, and y′ is 0 or 1. That isM_(y′) is at the 3′-end of the polynucleotide. An exemplary TLR9inhibitory motif is 5′-S₁S₂S₃S₄-3′, wherein each of S₁, S₂, S₃, and S₄are independently G or I (inosine or 2′-deoxyinosine). In someembodiments in which the TLR9 inhibitory motif is 5′-S₁S₂S₃S₄-3′, eachof S₁, S₂, S₃, and S₄ are independently G or a molecule that is capableof preventing G-tetrad formation and/or preventing Hoogsteen basepairing such as inosine, 7-deaza-guanosine, 7-deaza-2′-deoxyxanthosine,7-deaza-8-aza-2′-deoxyguanosine, 2′-deoxynebularine, isodeoxyguanosine,and 8-oxo-2′-deoxyguanosine.

Assays for assessing immunostimulatory activity are known in the art,and described in Examples B1 and B2. For the purpose of the presentdisclosure, immunostimulatory activity can be determined by measuringinterferon-alpha production by human peripheral blood mononuclear cellsafter incubation in the present and absence of a test compound. A testcompound is said to possess immunostimulatory activity when at leasttwo-fold more interferon-alpha is produced in the presence of the testcompound. It is understood that positive and negative controls areuseful in assays for immunostimulatory activity. A suitable negativecontrol for immunostimulatory activity is a medium alone. Anothersuitable negative control is a polynucleotide consisting of thenucleotide sequence 5′-TGACTGTGAA CCTTAGAGAT GA-3′ (D56-30 set forth asSEQ ID NO:5). A suitable positive control for immunostimulatory activityis a polynucleotide consisting of the nucleotide sequence 5′-TGACTGTGAACGTTCGAGAT GA-3′ (D56-10 set forth as SEQ ID NO:6).

II. Synthesis of Chimeric Compounds

The disclosure further provides methods for preparing the chimericcompounds (such as the branched chimeric compounds) detailed herein, aswell as compositions and intermediates useful therein.

In one aspect, the disclosure provides a method for making a branchedchimeric compound of formula (I):

[D-L¹-L²-(PEG)-L³]_(x)F  (I),

wherein:

D is a polynucleotide or a linear chimeric compound;

L¹ is a first linker comprising an alkylthio group;

L² is a second linker comprising a succinimide group;

L³ is a third linker comprising an amide group;

PEG is a polyethylene glycol (e.g., —(OCH₂CH₂)_(n)—, where n is aninteger from 2 to 80);

x is an integer from 3 to 300; and

F is a branched copolymer of sucrose and epichlorohydrin having amolecular weight of about 100,000 to about 700,000 daltons and isconnected to L³ via an ether group,

wherein the polynucleotide comprises the nucleotide sequence: 5′-TCGGCGCAACGTTC TCGGCGC-3′ (SEQ ID NO:1), wherein the polynucleotide is lessthan 50 nucleotides in length, and wherein one or more linkages betweenthe nucleotides and the linkage between the 3′-terminal nucleotide andL¹ are phosphorothioate ester linkages, and

wherein the linear chimeric compound comprises three polynucleotides andtwo hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinone or more of the linkages between the nucleotides, the linkagesbetween the nucleotides and the HEG spacers and the linkage between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages,

wherein the method comprises:

reacting a compound of the formula D-L^(1a)-SH, where D is as definedfor formula (I) and L^(1a) is (CH₂)_(m) where m is an integer from 2 to9, with a compound of formula (II):

[L^(2a)-(PEG)-L³]_(y)-F  (II)

wherein L³, PEG and F are as defined for formula (I);

L^(2a) is

and

y is an integer from 3 to 350.

In some embodiments, L^(2a) is

In some instances, every maleimide group in the compound of formula (II)is reacted with a nucleic acid moiety D. Thus in some embodiments, yequals to x. In other instances, only some of the maleimide groups inthe compound of formula (II) are reacted with a nucleic acid moiety D,while some are not reacted with a nucleic acid moiety D. Thus in someembodiments, y is an integer greater than x. In some embodiments, y isan integer greater than (lower limit) 3, 6, 9, 12, 20, 30, 40, 50, 60,70, 80, 90, 100, 110, 120, 130, 140, 150, 155, 165, 190 or 200. In someembodiments, y is an integer less than (upper limit) 350, 300, 275, 250,225, 215, 210, 205, 200, 190, 180, 160, 150, 140, 130, 120, 110, 100,90, 80, 70, 60 or 50. That y can be an integer in the range of fromabout 3 to 350 in which the lower limit is less than the upper limit.For example, in some embodiments, y is from 20 to 350, from 30 to 300,from 155 to 215, from 165 to 205, from 20 to 250, from 90 to 250, from120 to 250, from 120 to 220, from 160 to 220, from 20 to 200, from 60 to180, from 90 to 150, from 100 to 140, or from 110 to 130. In a preferredembodiment, y is about 190, about 185, about 150 or about 120. In someembodiments, y is about 190±30 or about 185±30. In some embodiments wheny is an integer greater than x, the maleimide groups that are notreacted with a nucleic acid moiety D are capped and/or hydrolyzed. Insome embodiments when y is an integer greater than x, the maleimidegroups that are not reacted with a nucleic acid moiety D are capped withcysteine and/or are hydrolyzed by water.

The reactive thiol compound D-L^(1a)-SH is often made from a more stabledisulfide compound prior to use. In some embodiment, the method furthercomprises reacting a disulfide compound of the formulaD-L^(1a)-SS-L^(1a)-OH with a reducing agent (e.g., a phosphinecompound). In some embodiments, D is as defined herein for formula (I)and L^(1a) is (CH₂)_(m) where m is an integer from 2 to 9. In some ofthe embodiments, m is 2, 3, 4, 5, 6, 7, 8 or 9. In some embodiments, mis from 3 to 6. In some of these embodiments, m is 3 or 6. In oneembodiment, m is 6. In one embodiment, m is 3. One example of thereducing agent is tris(2-carboxyethyl)phosphine hydrochloride (TCEP).

The present invention also provides a compound of the formulaD-L^(1a)-SH or a compound of the formula D-L^(1a)-SS-L^(1a)-OH, whereinD is a polynucleotide or a linear chimeric compound, such as apolynucleotide detailed herein or a linear chimeric compound detailedherein, and L^(1a) is (CH₂)_(m) where m is an integer from 2 to 9. Insome of these embodiments, D is a polynucleotide comprising thenucleotide sequence: 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ ID NO:1),wherein the polynucleotide of D is less than 50 nucleotides in length,and wherein one or more linkages between the nucleotides arephosphorothioate ester linkages. In some of these embodiments, D is alinear chimeric compound comprises three nucleic acid moieties and twohexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides, andwherein one or more linkages between the nucleotides, between thenucleotides and the HEG spacers and between the 3′-nucleotide and L¹ arephosphorothioate ester linkages. In some of these embodiments, D is alinear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2). In someembodiments, all of the internucleotide linkages, the linkages betweennucleotides and the HEG spacers, and the linkage between the 3′-terminalnucleotide and L¹ in the linear chimeric compound of D arephosphorothioate ester linkages. In some embodiments, the nucleic acidmoieties of the linear chimeric compound of D are a2′-deoxyribonucleotide. In some of the embodiments, m is 2, 3, 4, 5, 6,7, 8 or 9. In some embodiments, m is from 3 to 6. In some of theseembodiments, m is 3 or 6. In one embodiment, m is 6. In one embodiment,m is 3.

In some embodiments, D-L^(1a)-SH is5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′-(CH₂)_(m)—SH (SEQ IDNO:2), where m is an integer from 2 to 9. In some embodiments,D-L^(1a)-SS-L^(1a)-OH is5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′-(CH₂)_(m)—SS—(CH₂)_(m)—OH(SEQ ID NO:2), where m is an integer from 2 to 9. In some of theseembodiments, m is 3 or 6. In one embodiment, m is 6. In one embodiment,m is 3.

The polynucleotides, linear chimeric compounds and disulfide modifiednucleic acids described herein may be prepared using methods known inthe art, such as methods descried in U.S. Pat. No. 8,114,418. Forexample, the polynucleotides can be manufactured by solid phasesynthesis using phosphoramidite chemistry with oxidative sulfurization,purified and isolated according to the manufacturer's protocols(Molecules 2013, 18, 14268-14284). Examples of nucleoside monomers usedwere 5′-dimethoxytrityl-protected-2′-deoxynucleoside. The linearchimeric compounds are made by incorporating the HEG spacer (e.g., SpacePhorphoramidite 18 from Glen Research, Sterling, Va.) in thepolynucleotide. In some embodiments, the polynucleotides and/or thelinear chimeric compounds are synthesized on a solid phase synthesizerprogrammed to add the nucleotide monomers, HEG spacers and linkers inthe desired order, with the synthesis occurring in the 3′ to 5′direction. The 3′-nucleoside or linker group (e.g., 3′-Thiol-Modifier C6S-S CPG) is attached to the solid support. In some embodiments, thesynthesis cycle consists of a detritylation step using acid (e.g.,dichloroacetic acid in toluene), a coupling step using thephosphoramidite monomer plus a mildly acidic activator (e.g., saccharin1-methylimidazole), an oxidative sulfurization step (e.g., 0.2 MXanthane Hydride in pyridine), and a capping step for unreacted groups(e.g., isobutyric anhydride and N-methylimidazole). The synthesis cycleis repeated until the PN and CC sequence was fully assembled. Theprotected polynucleotide and chimeric compound can be cleaved anddeprotected from the solid support (e.g., removal of cyanoethylphosphate protecting groups using 20% t-butylamine in acetonitrile,followed by treatment with concentrated aqueous ammonia to cleave PN orCC from support, and holding the resulting solution for 72 hours atambient temperature to remove the protecting groups on the nucleotides).The polynucleotides can be purified (e.g., using anion exchangechromatography), desalted (e.g., by ultrafiltration/diafiltration usinga tangential flow filtration system), lyophilized, and stored frozen aslyophilized solids.

The PEG in the compound of the formula (II) can be introduced via anamine derivative of the multivalent polysaccharide F reacting with anactivated ester compound comprising the PEG. In some embodiments, themethod of making a compound of formula (I) further comprises reacting acompound of the formula (III):

[NH₂CH₂CH₂NHC(O)CH₂]_(z)—F  (III)

wherein F is as defined for formula (I) and z is an integer from 3 to400,

with a compound of the formula L^(2a)-(PEG)-L^(3a)-Lv, where L^(2a) andPEG are as defined for formula (II); L^(3a) is —NHC(O)CH₂CH₂C(O)— or—C(O)—; and Lv is a leaving group,

to form the compound of the formula (II).

In some embodiments, the activated ester compound comprising the PEG isan N-hydroxysuccinimide (NHS or HOSu) ester, and Lv is(2,5-dioxopyrrolidin-1-yl)oxy (i.e., OSu). Other activated carboxylicacid or esters known in the art can be used to react with the amine offormula (III) to form the compound of formula (II).

In some embodiments, F is a branched copolymer of sucrose andepichlorohydrin having a molecular weight of about 100,000 to 700,000 inDaltons. In some embodiments, F is a branched copolymer of sucrose andepichlorohydrin having a molecular weight of about 400,000±100,000Daltons (e.g., a FICOLL® PM 400), and the compound of formula (III) is acompound of AECM-FICOLL®400. Depending on the relative amounts of theactivated ester L^(2a)-(PEG)-L^(3a)-Lv (e.g., an NHS esterL^(2a)-(PEG)-L^(3a)-OSu) to the compound of formula (III) (e.g., acompound of AECM-FICOLL®400) used, some or all of the amino groups inthe compound of formula (III) may be PEGylated. Thus in someembodiments, z equals to y. In some embodiments, z is an integer greaterthan y. In some embodiments, z is an integer greater than (lower limit)3, 6, 9, 12, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140,150, 155, 165, 190 or 200. In some embodiments, z is an integer lessthan (upper limit) 400, 350, 300, 275, 250, 225, 215, 210, 205, 200,190, 180, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60 or 50. Thatz can be an integer in the range of from about 3 to 400 in which thelower limit is less than the upper limit. For example, in someembodiments, z is from 20 to 400, from 50 to 300, from 190 to 250, from200 to 240, from 20 to 350, from 30 to 300, from 155 to 215, from 165 to205, from 20 to 250, from 90 to 250, from 120 to 250, from 120 to 220,from 160 to 220, from 20 to 200, from 60 to 180, from 90 to 150, from100 to 140, or from 110 to 130. In a preferred embodiment, z is about220, about 190, about 150 or about 120. In some embodiments, z is about220±30 or about 220±20. In some embodiments when z is an integer greaterthan y, excess amines are capped. In some embodiments when z is aninteger greater than y, excess amines are capped with sulfo-NHS-acetateor NHS-acetate.

FICOLL® is synthesized by cross-linking sucrose with epichlorohydrinwhich results in a highly branched structure.Aminoethylcarboxymethyl-FICOLL (AECM-FICOLL®) can be prepared by themethod of Inman, 1975, J. Imm. 114:704-709. AECM-FICOLL can then bereacted with a heterobifunctional crosslinking reagent, such as6-maleimido caproic acyl N-hydroxysuccinimide ester, and then conjugatedto a thiol-derivatized nucleic acid moiety (see Lee et al., 1980, Mol.Imm. 17:749-56). Other polysaccharides may be modified similarly.

The NHS ester (L^(2a)-(PEG)-L^(3a)-OSu) used in the method may beobtained from commercial sources or made by methods known in the art.

In some embodiments, provided is a compound of formula (II):

[L^(2a)-(PEG)-L³]_(y)-F  (II)

wherein:

L^(2a) is a moiety comprising a maleimide group;

L³ is a linker comprising an amide group;

PEG is a polyethylene glycol;

y is an integer from 3 to 350; and

F is a branched copolymer of sucrose and epichlorohydrin and isconnected to L³ via an ether group.

In some embodiments of the compounds of formula (II), L³, PEG and F areas defined for formula (I) or any variations detailed herein;

L^(2a) is

wherein L^(2b) is as detailed herein for formula (I) or any variationsthereof (e.g., —CH₂CH₂C(O)NHCH₂CH₂CH₂—, —CH₂CH₂C(O)NHCH₂CH₂—, —CH₂CH₂—or —CH₂CH₂CH₂CH₂—); and

y is as detailed herein for formula (II).

For example, in some embodiments of the compounds of formula (II), F hasa molecular weight of from about 300,000 to 500,000 daltons (e.g.,FICOLL® PM 400 of GE Healthcare). In some embodiments, y is an integergreater than (lower limit) 3, 6, 9, 12, 20, 30, 40, 50, 60, 70, 80, 90,100, 110, 120, 130, 140 or 150. In some embodiments, y is an integergreater than (lower limit) 3, 6, 9, 12, 20, 30, 40, 50, 60, 70, 80, 90,100, 110, 120, 130, 140, 150, 155, 165, 190 or 200. In some embodiments,y is an integer less than (upper limit) 350, 300, 275, 250, 225, 215,210, 205, 200, 190, 180, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70,60 or 50. That y can be an integer in the range of from about 3 to 350in which the lower limit is less than the upper limit. For example, insome embodiments, y is from 20 to 350, from 30 to 300, from 155 to 215,from 165 to 205, from 20 to 250, from 90 to 250, from 120 to 250, from120 to 220, from 160 to 220, from 20 to 200, from 60 to 180, from 90 to150, from 100 to 140, or from 110 to 130. In a preferred embodiment, yis about 190, about 185, about 150 or about 120. In some embodiments, yis about 190±30 or about 185±30. In some embodiments, PEG is of theformula —(OCH₂CH₂)_(n)—, where n is an integer from 2 to 80. In apreferred embodiment, PEG is —(OCH₂CH₂)₆—. In some embodiments, L^(2a)is

In some embodiments, L³ is of the formula

wherein L^(3a) is a spacer capable of linking an alkyl group and anamine, such as a spacer of the formula —NHC(O)CH₂CH₂C(O)— or —C(O)—.

In some embodiments, provided is a method for making a compound offormula (II):

[L^(2a)-(PEG)-L³]_(y)-F  (II)

wherein:

L^(2a) is a moiety comprising a maleimide group;

L³ is a linker comprising an amide group;

PEG is a polyethylene glycol (e.g., —(OCH₂CH₂)_(n)—, where n is aninteger from 2 to 80);

y is an integer from 3 to 350; and

F is a branched copolymer of sucrose and epichlorohydrin and isconnected to L³ via an ether group,

the method comprising reacting a compound of the formula (III):

[NH₂CH₂CH₂NHC(O)CH₂]_(z)—F  (III)

wherein F is as defined for formula (II) and z is an integer from 3 to400,

with a compound of the formula L^(2a)-(PEG)-L^(3a)-Lv, where L^(2a) andPEG are as defined for formula (II); L^(3a) is —NHC(O)CH₂CH₂C(O)—,—OC(O)— or —C(O)—; and Lv is a leaving group (e.g.,(2,5-dioxopyrrolidin-1-yl)oxy).

In some embodiments, provided is composition comprising a heterogeneousmixture of compounds of formula (II), wherein L^(2a), PEG, L³, F and yare independently as described herein for formula (II), wherein the Fmoieties of the heterogeneous mixture of compounds of formula (II) havean average molecular weight between about 200,000 and about 600,000 inDaltons, and wherein the compounds of formula (II) in the heterogeneousmixture have an average loading ratio (y) between about 60 and about250. In some embodiments, the F moieties of the heterogeneous mixture ofcompounds of formula (II) have an average molecular weight between about300,000 and about 500,000 in Daltons. In some embodiments, the Fmoieties of the heterogeneous mixture of compounds of formula (II) havean average molecular weight of about 400,000±100,000 Daltons. In someembodiments, the compounds of formula (II) in the heterogeneous mixturehave an average loading ratio (y) between about 60 and about 250,between about 90 and about 250, between about 120 and about 250, betweenabout 120 and about 220, between about 160 and about 220, between about60 and about 200, between about 60 and about 180, or between about 90and about 150. In some embodiments, the compounds of formula (II) in theheterogeneous mixture have an average loading ratio (y) of about 120±30,about 150±30, about 185±30 or about 190±30. In some embodiments, thecomposition comprises a heterogeneous mixture of compounds of formula(II), wherein L^(2a), PEG, L³, F and y are independently as describedherein for formula (II), wherein the F moieties of the heterogeneousmixture of compounds of formula (II) have an average molecular weight ofabout 400,000±100,000 Daltons, and wherein the compounds of formula (II)in the heterogeneous mixture have an average loading ratio (y) of about120±30, about 150±30, about 185±30 or about 190±30.

The present invention also provides a method for making a mixturecomprising a distribution of compounds of formula (I) detailed hereinfrom a distribution of compounds of formula (II) detailed herein. In oneaspect, provided is a method for making a heterogeneous mixture ofbranched chimeric compounds of formula (I):

[D-L¹-L²-(PEG)-L³]_(x)-F  (I)

wherein:

D is independently a polynucleotide or a linear chimeric compound;

L¹ is independently a first linker comprising an alkylthio group;

L² is independently a second linker comprising a succinimide group;

L³ is independently a third linker comprising an amide group;

PEG is independently a polyethylene glycol (e.g., —(OCH₂CH₂)_(n)—, wheren is an integer from 2 to 80);

x is independently an integer from 3 to 300; and

F is independently a branched copolymer of sucrose and epichlorohydrinhaving a molecular weight of about 100,000 to about 700,000 and isconnected to L³ via an ether group,

wherein the polynucleotide comprises the nucleotide sequence: 5′-TCGGCGCAACGTTC TCGGCGC-3′ (SEQ ID NO:1), wherein the polynucleotide isindependently less than 50 nucleotides in length, and wherein one ormore linkages between the nucleotides and the linkage between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages, and

wherein the linear chimeric compound independently comprises threepolynucleotides and two hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinone or more of the linkages between the nucleotides, the linkagesbetween the nucleotides and the HEG spacers and the linkage between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages,

the method comprises:

reacting a composition comprising compounds of the formula D-L^(1a)-SH,where D is independently as defined for formula (I) and L^(1a) is(CH₂)_(m) where m is independently an integer from 2 to 9, with acomposition comprising a heterogeneous mixture of compounds of formula(II):

[L^(2a)-(PEG)-L³]_(y)-F  (II)

wherein L³, PEG and F are independently as defined for formula (I);

each L^(2a) is independently

and

y is independently an integer from 3 to 350;

and wherein the composition comprising compounds of formula (II)comprises a heterogeneous mixture of compounds of formula (II), whereinthe F moieties of the heterogeneous mixture of compounds of formula (II)have an average molecular weight between about 200,000 and about 600,000in Daltons, and wherein the compounds of formula (II) in the mixturehave an average loading ratio (y) between about 60 and about 250. Insome embodiments, the F moieties of the heterogeneous mixture ofcompounds of formula (II) have an average molecular weight of about400,000±100,000 Daltons. In some embodiments, the compounds of formula(II) in the heterogeneous mixture have an average loading ratio (y) ofabout 120±30, about 150±30, about 185±30 or about 190±30.

In some embodiments, each L^(2a) is independently

In some embodiments, provided is a method for making a compositioncomprising a heterogeneous mixture of compounds of formula (II):

[L^(2a)-(PEG)-L³]_(y)-F  (II)

wherein:

L^(2a) is independently a moiety comprising a maleimide group;

L³ is independently a linker comprising an amide group;

PEG is independently a polyethylene glycol (e.g., —(OCH₂CH₂)_(n)—, wheren is an integer from 2 to 80);

y is independently an integer from 3 to 350; and

F is independently a branched copolymer of sucrose and epichlorohydrinand is connected to L³ via an ether group,

comprising reacting a composition comprising a mixture of compounds ofthe formula (III):

[NH₂CH₂CH₂NHC(O)CH₂]_(z)—F  (III)

wherein F is as defined for formula (II) and z is independently aninteger from 3 to 400,

with a compound of the formula L^(2a)-(PEG)-L^(3a)-Lv, where L^(2a) andPEG are as defined for formula (II); L^(3a) is —NHC(O)CH₂CH₂C(O)—,—OC(O)— or —C(O)—; and Lv is a leaving group (e.g.,(2,5-dioxopyrrolidin-1-yl)oxy),

and wherein the F moieties of the mixture of compounds of formula (III)have an average molecular weight between about 200,000 and about 600,000daltons, and the mixture of compounds of the formula (III) have anaverage loading ratio (z) between about 60 and about 280.

In some embodiments of the method for making a composition comprising aheterogeneous mixture of compounds of formula (II), L^(2a), PEG, L^(3a)and Lv are as detailed herein, and wherein the F moieties of the mixtureof compounds of formula (III) have an average molecular weight betweenabout 300,000 and about 500,000 in Daltons. In some embodiments, the Fmoieties of the mixture of compounds of formula (III) have an averagemolecular weight of about 400,000±100,000 Daltons. In some embodiments,the mixture of compounds of the formula (III) have an average loadingratio (z) between about 50 and about 350, between about 50 and about280, between about 60 and about 250, between about 60 and about 180,between about 60 and about 150, between about 90 and about 280, betweenabout 90 and about 250, between about 90 and about 200, between about 90and about 150, between about 120 and about 280, between about 120 andabout 250, between about 150 and about 280, between about 150 and about250, between about 180 and about 280, between about 180 and about 250,between about 200 and about 250 or between about 210 and about 230. Insome embodiments, the mixture of compounds of the formula (III) have anaverage loading ratio (z) of about 120±30, about 150±30, about 180±30,about 220±30 or about 220±20. In some embodiments, the mixture ofcompounds of formula (III) is AECM FICOLL® 400.

In some embodiments, the method for making a heterogeneous mixture ofbranched chimeric compounds of formula (I) further comprises reacting acomposition comprising a mixture of compounds of the formula (III) asdetailed herein with a compound of the formula L^(2a)-(PEG)-L^(3a)-Lv asdetailed herein.

In some embodiments, the methods of making a compound of formula (I) ora composition comprising a heterogeneous mixture of compounds of formula(I) further comprise purifying the chimeric compounds of formula (I),and/or any of the intermediate compounds such as compounds of formula(II) and compounds of formula (III). In some embodiments, the methodfurther comprises purifying the chimeric compounds of formula (I) bydiafiltration. In some embodiments, the method further comprisespurifying the chimeric compounds of formula (I) by diafiltration using a100,000 molecular weight cut off (MWCO) membrane.

III. Pharmaceutical Compositions

Pharmaceutical compositions comprising a polynucleotide, linear chimericcompound or branched chimeric compound (e.g., active agent) of thepresent disclosure are also provided. The pharmaceutical compositionsroutinely contain a pharmaceutically acceptable excipient. In someembodiments, the pharmaceutical compositions further comprise anantigen. Pharmaceutical compositions of the present disclosure may be inthe form of a solution or a freeze dried solid. The pharmaceuticalcompositions of the present disclosure are preferably sterile, andpreferably essentially endotoxin-free.

A. Excipients

Pharmaceutically acceptable excipients of the present disclosure includefor instance, solvents, bulking agents, buffering agents, tonicityadjusting agents, and preservatives (see, e.g., Pramanick et al., PharmaTimes, 45:65-77, 2013). In some embodiments the pharmaceuticalcompositions may comprise an excipient that functions as one or more ofa solvent, a bulking agent, a buffering agent, and a tonicity adjustingagent (e.g., sodium chloride in saline may serve as both an aqueousvehicle and a tonicity adjusting agent). The pharmaceutical compositionsof the present disclosure are suitable for parenteral administration.That is the pharmaceutical compositions of the present disclosure arenot intended for enteral administration.

In some embodiments, the pharmaceutical compositions comprise an aqueousvehicle as a solvent. Suitable vehicles include for instance sterilewater, saline solution, phosphate buffered saline, and Ringer'ssolution. In some embodiments, the composition is isotonic orhypertonic.

The pharmaceutical compositions may comprise a bulking agent. Bulkingagents are particularly useful when the pharmaceutical composition is tobe lyophilized before administration. In some embodiments, the bulkingagent is a lyoprotectant that aids in the stabilization and preventionof degradation of the active agents during freeze-drying and/or duringstorage. Suitable bulking agents are sugars (mono-, di- andpolysaccharides) such as sucrose, lactose, trehalose, mannitol,sorbital, glucose and raffinose.

The pharmaceutical compositions may comprise a buffering agent.Buffering agents control pH to inhibit degradation of the active agentduring processing, storage and optionally reconstitution. Suitablebuffers include for instance salts comprising acetate, citrate,phosphate or sulfate. Other suitable buffers include for instance aminoacids such as arginine, glycine, histidine, and lysine. The bufferingagent may further comprise hydrochloric acid or sodium hydroxide. Insome embodiments, the buffering agent maintains the pH of thecomposition within a range of 4 to 9. In some embodiments, the pH isgreater than (lower limit) 4, 5, 6, 7 or 8. In some embodiments, the pHis less than (upper limit) 9, 8, 7, 6 or 5. That is, the pH is in therange of from about 4.0 to 9.0 in which the lower limit is less than theupper limit.

The pharmaceutical compositions may comprise a tonicity adjusting agent.Suitable tonicity adjusting agents include for instance dextrose,glycerol, sodium chloride, glycerin and mannitol.

The pharmaceutical compositions may comprise a preservative. Suitablepreservatives include for instance antioxidants and antimicrobialagents. However, in preferred embodiments, the pharmaceuticalcomposition is prepared under sterile conditions and is in a single usecontainer, and thus does not necessitate inclusion of a preservative.

B. Antigens

The present disclosure further provides pharmaceutical compositionscomprising an antigen and an excipient in addition to a polynucleotide,linear chimeric compound or branched chimeric compound. In thecompositions of the present disclosure comprising an antigen, theantigen is not covalently-linked to the polynucleotide, the linearchimeric compound or the branched chimeric compound. In some preferredembodiments, the antigen is a protein antigen. In some preferredembodiments, the antigen is a polysaccharide antigen, which ispreferably covalently attached to a carrier protein. In someembodiments, the antigen is a microbial antigen, an allergen or a tumorantigen.

The pharmaceutical compositions may comprise a microbial antigenselected from the group consisting of a viral antigen, a bacterialantigen, a fungal antigen and a parasite antigen. In some embodiments,the microbial antigen is from a microbe that causes an infectiousdisease in a nonhuman, mammalian subject. In some embodiments, themicrobial antigen is from a microbe that causes an infectious disease ina human subject. In some embodiments, the infectious disease is causedby a virus, a bacterium, a fungus or a protozoan parasite. Suitablemicrobial antigens include for instance antigens of adenovirus type 4,adenovirus type 7, anthrax, Mycobacterium tuberculosis, Corynebacteriumdiphtheriae (e.g., diphtheria toxoid), Clostridium tetani (e.g., tetanustoxoid), Bordetella pertussis, Haemophilus influenzae type B, hepatitisA virus, hepatitis B virus (e.g., HBsAg), human papillomavirus (types 6,11, 16, 18, 31, 33, 45, 52 and 58) influenza virus type A and B (e.g.,haemagglutinin, neuraminadase), influenza virus type B, parainfluenzavirus, Japanese encephalitis virus, measles virus, mumps virus, rubellavirus, Neisseria menigitidis (Groups A, B, C, Y and W-135),Streptococcus pneumoniae (serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C,19A, 19F and 23F), poliovirus, rabies virus, rotavirus, vaccinia virus,Salmonella typhi, varicella zoster virus, and yellow fever virus (see,e.g., “www.fda.gov/BiologicsBloodVaccines/Vaccines”). In someembodiments, the microbial antigen is a viral antigen of Herpes simplexvirus type 1 or 2, human herpes virus, human immunodeficiency virus type1, and respiratory syncytial virus. In some embodiments, the microbialantigen is a fungal antigen of Candida albicans, Aspergillus flavus,Cryptococcus neoformans, Histoplasma capsulatum, and Pneumocystiscarinii. In some embodiments, the microbial antigen is a parasiteantigen of a Leishmania species, a Plasmodium species, a Schistosomaspecies. or a Trypanosoma species.

The pharmaceutical compositions may comprise an allergen. In someembodiments, the allergen is an environmental antigen such as mammalian,insect, plant and mold allergens. In some embodiments, the mammalianallergen includes fur and dander. Suitable mammalian allergens includefor instance, cat Fel d 1, cow Bos d 2, dog Can f I and Can f II, horseEqu c1, and mouse MUP. In some embodiments, the insect allergen includesinsect feces and venom. Exemplary insect allergens include ant Sol i2,bee PLA and Hya, cockroach Bla g Bd9OK, Bla g4, GST, and Per a3, dustmite Der p2, Der f2, Der p10, and Tyr p2, hornet Dol m V, mosquito Aed a1, and yellow jacket hyaluronidase and phospholipase. In someembodiments, the plant allergen includes grass, weed and tree allergens(e.g., pollens). Suitable grass allergens include for instance,allergens of Kentucky bluegrass, meadow fescue, orchard grass, redtopgrass, perennial ryegrass, sweet vernal grass and timothy. Exemplaryplant allergens include barley Hor v 9, birch Bet v1 and v2, cherry Prua 1, corn Zml3, grass Phl p 1, 2, 4, 5, 6, 7, 11 and 12, Hol 1 5, Cyn d7 and d12, cedar Jun a 2, Cry j 1 and j2, juniper Jun o2, latex Hey b7,yellow mustard Sin a I, rapeseed Bra r 1, ragweed Amb a 1, and rye Lolp1. In some embodiments, the mold allergen is an Aspergillus fumigatusallergen such as Asp f 1, 2, 3, 4 and 6. In some embodiments theallergen is a food allergen such as a shell fish allergen, a legumeallergen, a nut allergen or a milk allergen. Exemplary food allergensinclude shrimp tropomyosin, peanut Ara h 1, 2, 3, 8 and 9, walnut Jug r1 and 3, hazelnut Cor a 1, 14 and 8 LTP, cow's milk lactalbumin, caseinand lactoferrin.

The pharmaceutical compositions may comprise a tumor antigen. In someembodiments, the tumor antigen is a mammalian antigen. Suitable tumorantigens have been described in the art (see, e.g., Cheever et al.,Clinical Cancer Research, 15:5323-5337, 2009). For instance, suitabletumor antigens include WT1, MUC1, LMP2, HPV E6 E7, EGFRvIII, Her-2/neu,idiotype, MAGE A3, p53, NY-ESO-1, PSMA, GD2, CEA, MelanA/Martl, Ras,gp100, proteinase3 (PR1), bcr-able, tyrosinase, survivin, PSA, hTERT,sarcoma translocation breakpoints, EphA2, PAP, MP-IAP, AFP, EpCAM, ERG,NA17, PAX3, ALK, androgen receptor, cyclin B1, polysialic acid, MYCN,PhoC, TRP-2, GD3, Fucosyl, GM1, mesothelin, PSCA, MAGE A1, sLe(a),CYP1B1, PLAC1, GM3, BORIS, Tn, GloboH, ETV6-AML, NY-BR-1, RGS5, SART3,STn, cabonic anhydrase IX, PAX5, OY-TES 1, sperm protein 17, LCK,HMWMAA, AKAP-4, SSX2, XAGE 1, B7H3, legumain, Tie 2, Page4, VEGFR2,MAD-CT-1, FAP, PDGFR-beta, MAD-CT-2, and Fos-related antigen 1.

IV. Methods of Use

The pharmaceutical compositions of the present disclosure are suitablefor a plurality of uses involving modulating an immune response in amammalian subject in need thereof. Mammalian subjects include but arenot limited to humans, nonhuman primates, rodents, pets, and farmanimals. In some embodiments, modulating an immune response comprisesstimulating an immune response. In some embodiments, modulating animmune response comprises inhibiting an immune response. In someembodiments, the pharmaceutical compositions may be administered to thesubject in an amount effective to achieve a specific outcome.

A. Dosage and Mode of Administration

As with all pharmaceutical compositions, the effective amount and modeof administration may vary based on several factors evident to oneskilled in the art. Factors to be considered include whether thepharmaceutical composition contains a polynucleotide, a linear chimericcompound or a branched chimeric compound (e.g., active agents), andwhether the pharmaceutical composition further contains an antigen. Ingeneral, dosages of multivalent active agents such as branched chimericcompounds are lower than dosages of monovalent active agents such aspolynucleotides and linear chimeric compounds. Other factors to beconsidered include the outcome to be achieved, and the number of dosesto be administered.

A suitable dosage range is one that provides the desired effect. Dosagemay be determined by the amount of polynucleotide, linear chimericcompound or branched chimeric compound administered to the subject. Anexemplary dosage range of the polynucleotide, linear chimeric compoundor branched chimeric compound given in amount to be delivered by subjectweight is from about 1 to 1000 mcg/kg. In some embodiments, the dosageis greater than about (lower limit) 1, 5, 10, 50, 100, 150, 200, 250,300, 350, 400, 450 or 500 mcg/kg. In some embodiments, the dosage isless than about (upper limit) 1000, 900, 800, 700, 600, 500, 450, 400,350, 300, 250, 200, 150, or 100 mcg/kg. That is, the dosage is anywherein the range of from about 1 to 1000 mcg/kg in which the lower limit isless than the upper limit. An exemplary dosage range of thepolynucleotide, linear chimeric compound or branched chimeric compoundgiven in amount to be delivered to a subject is from about 100 to 5000mcg. In some embodiments, the dosage is greater than about (lower limit)100, 500, 1000, 1500, 2000, 2500, 3000, 3500 or 4000 mcg. In someembodiments, the dosage is less than about (upper limit) 5000, 4500,4000, 3500, 3000, 2500, 2000, 1500, or 1000 mcg. That is, the dosage isanywhere in the range of from about 100 to 5000 mcg in which the lowerlimit is less than the upper limit.

In some embodiments, when the pharmaceutical composition furthercomprises an antigen, the antigen dosage range given in amount to bedelivered to a subject is from about 1 mcg to 50 mcg. In someembodiments, the antigen dosage is greater than about (lower limit) 1,5, 10, 15, 20, 25, 30, 35 or 40 mcg. In some embodiments, the antigendosage is less than about (upper limit) 50, 45, 40, 35, 30, 25, 20, 15,or 10 mcg. That is, the antigen dosage is anywhere in the range of fromabout 1 to 50 mcg in which the lower limit is less than the upper limit.

Likewise, a suitable route of administration is one that provides thedesired effect. In general, the pharmaceutical compositions of thepresent disclosure are intended for parenteral administration (e.g., notoral or rectal administration). Suitable routes of administrationinclude injection, topical and inhalation. In particular, thepharmaceutical compositions of the present disclosure may beadministered by a route such as intramuscular, subcutaneous, intravenousepidermal (gene gun), transdermal, and inhalation. Devices suitable foradministration by inhalation include, for instance atomizers,vaporizers, nebulizers, and dry powder inhalation delivery devices. Insome embodiments, when the pharmaceutical compositions are intended totreat a solid tumor, the compositions are administered intratumorally.

A suitable dosing regimen is one that provides the desired effect in aprophylactic or therapeutic context. The number of doses administered bya chosen route may be one or more than one. Frequency of dosing mayrange from weekly, bi-weekly, monthly, bi-monthly, or 3 to 12 monthsbetween doses. In some embodiments, 2 doses are administered with thesecond dose being administered one to two months after the first dose.In some embodiments, 3 doses are administered with the second dose beingadministered one to two months after the first dose, and the third dosebeing administered one to five months after the second dose. In otherembodiments, 3, or 4 doses may be administered on a bi-weekly or monthlybasis. In other embodiments, a shorter or longer period of time mayelapse in between doses. In certain embodiments, the interval betweensuccessive dosages may vary in terms of number of weeks or number ofmonths. In one embodiment, a series of 2, 3, 4, 5, or 6 weekly doses maybe administered followed by a second series of a number of weekly dosesat a later time point. One of skill in the art will be able to adjustthe dosage regiment by measuring biological outcomes as exemplified inthe Examples, such as antigen-specific antibody responses or tumorregression.

B. Stimulation of an Immune Response

The pharmaceutical compositions of the present disclosure are suitablefor a plurality of uses involving modulating an immune response in amammalian subject in need thereof. In some embodiments, the mammaliansubject is a human patient. In some embodiments, the pharmaceuticalcompositions are used to stimulate an immune response in a mammaliansubject. In some embodiments, the pharmaceutical compositions are usedto inhibit an immune response in a mammalian subject. In someembodiments, the pharmaceutical compositions are administered to thesubject so as to achieve a specific outcome.

In brief, the present disclosure provides methods of stimulating animmune response in a mammalian subject, comprising administering to amammalian subject a pharmaceutical composition in an amount sufficientto stimulate an immune response in the mammalian subject. “Stimulating”an immune response, means increasing the immune response, which canarise from eliciting a de novo immune response (e.g., as a consequenceof an initial vaccination regimen) or enhancing an existing immuneresponse (e.g., as a consequence of a booster vaccination regimen). Insome embodiments, stimulating an immune response comprises one or moreof the group consisting of: stimulating IFN-alpha production;stimulating IL-6 production; stimulating B lymphocyte proliferation;stimulating interferon pathway-associated gene expression; stimulatingchemoattractant-associated gene expression; and stimulating plasmacytoiddendritic cell (pDC) maturation. Methods for measuring stimulation of animmune response are known in the art and described in the biologicalexamples of the present disclosure. In embodiments in which thepharmaceutical composition further comprises an antigen, stimulating animmune response comprises inducing an antigen-specific antibodyresponse.

For instance, in some embodiments in which the pharmaceuticalcomposition further comprises an antigen, the present disclosureprovides methods of inducing an antigen-specific antibody response in amammalian subject by administering to a mammalian subject thepharmaceutical composition in an amount sufficient to induce anantigen-specific antibody response in the mammalian subject. “Inducing”an antigen-specific antibody response means increasing titer of theantigen-specific antibodies above a threshold level such as apre-administration baseline titer or a seroprotective level.

The present disclosure further provides methods of preventing aninfectious disease in a mammalian subject, comprising administering to amammalian subject a pharmaceutical composition in an amount sufficientto prevent an infectious disease in the mammalian subject. That is, insome embodiments, the present disclosure provides prophylactic vaccines.In some embodiments, the mammalian subject is at risk of exposure to aninfectious agent. “Preventing” an infectious disease means to protect asubject from developing an infectious disease. In some embodiments,preventing an infectious disease further comprises protecting a subjectfrom being infected with an infectious agent (e.g., protecting a subjectfrom developing an acute or a chronic infection). Additionally thepresent disclosure provides methods of ameliorating a symptom of aninfectious disease in a mammalian subject, comprising administering to amammalian subject a pharmaceutical composition in an amount sufficientto ameliorate a symptom of an infectious disease in the mammaliansubject. That is, in some embodiments the present disclosure providestherapeutic vaccines. In some embodiments, the subject is acutely orchronically infected with an infectious agent. The infectious diseasemay be a viral, bacterial, fungal or parasitic disease. In someembodiments, the pharmaceutical composition may further comprise aviral, bacterial, fungal or parasitic antigen. “Ameliorating” a symptomof an infectious disease means to improve a symptom, preferablydiminishing extent of the disease.

Moreover the present disclosure provides methods of ameliorating asymptom of an IgE-related disorder in a mammalian subject, comprisingadministering to the mammalian subject a pharmaceutical composition inan amount sufficient to ameliorate a symptom of an IgE-related disorderin the mammalian subject. In some preferred embodiments, the IgE-relateddisorder is an allergy. Allergies include but are not limited toallergic rhinitis (hay fever), sinusitis, eczema, and hives. In someembodiments, the pharmaceutical composition may further comprise anallergen. “Ameliorating” a symptom of an IgE-related disorder means toimprove a symptom, preferably diminishing extent of the disorder. Forinstance, if the IgE-related disorder is allergic rhinitis, amelioratinga symptom means to reduce swelling of nasal mucosa, reduce rhinorrhea(runny nose), and/or reduce sneezing.

Furthermore, the present disclosure provides methods of treating cancerin a mammalian subject, comprising administering to a mammalian subjecta pharmaceutical composition in an amount sufficient to treat cancer inthe mammalian subject. “Treating” cancer means to bring about abeneficial clinical result such as causing remission or otherwiseprolonging survival as compared to expected survival in the absence oftreatment. In some embodiments, when the cancer is a solid tumor,“treating” cancer comprises shrinking the size of the solid tumor orotherwise reducing viable cancer cell numbers. In other embodiments,when the cancer is a solid tumor, “treating” cancer comprises delayinggrowth of the solid tumor.

Analysis (both qualitative and quantitative) of the immune response canbe by any method known in the art, including, but not limited to,measuring antigen-specific antibody production (including measuringspecific antibody subclasses), activation of specific populations oflymphocytes such as B cells and helper T cells, production of cytokinessuch as IFN-alpha, IL-6, IL-12 and/or release of histamine. Methods formeasuring antigen-specific antibody responses include enzyme-linkedimmunosorbent assay (ELISA). Activation of specific populations oflymphocytes can be measured by proliferation assays, and withfluorescence-activated cell sorting (FACS). Production of cytokines canalso be measured by ELISA.

Preferably, a Th1-type immune response is stimulated (i.e., elicited orenhanced). With reference to present disclosure, stimulating a Th1-typeimmune response can be determined in vitro or ex vivo by measuringcytokine production from cells treated with an active agent of thepresent disclosure (polynucleotide, linear chimeric compound or branchedchimeric compound) as compared to control cells not treated with theactive agent. Examples of “Th1-type cytokines” include, but are notlimited to, IL-2, IL-12, IFN-gamma and IFN-alpha. In contrast, “Th2-typecytokines” include, but are not limited to, IL-4, IL-5, and IL-13. Cellsuseful for the determination of immunostimulatory activity include cellsof the immune system, such as antigen presenting cells lymphocytes,preferably macrophages and T cells. Suitable immune cells includeprimary cells such as peripheral blood mononuclear cells, includingplasmacytoid dendritic cells and B cells, or splenocytes isolated from amammalian subject.

Stimulating a Th1-type immune response can also be determined in amammalian subject treated with an active agent of the present disclosure(polynucleotide, linear chimeric compound or branched chimeric compound)by measuring levels of IL-2, IL-12, and interferon before and afteradministration or as compared to a control subject not treated with theactive agent. Stimulating a Th1-type immune response can also bedetermined by measuring the ratio of Th1-type to Th2-type antibodytiters. “Th1-type” antibodies include human IgG1 and IgG3, and murineIgG2a. In contrast, “Th2-type” antibodies include human IgG2, IgG4 andIgE and murine IgG1 and IgE.

In some embodiments, the present disclosure provides kits that comprisea pharmaceutical composition (comprising an excipient and apolynucleotide, a linear chimeric compound or a branched chimericcompound) and a set of instructions relating to the use of thecomposition for the methods describe herein. The pharmaceuticalcomposition of the kits is packaged appropriately. For example, if thepharmaceutical composition is a freeze-dried power, a vial with aresilient stopper is normally used so that the powder may be easilyresuspended by injecting fluid through the resilient stopper. In someembodiments, the kits further comprise a device for administration(e.g., syringe and needle) of the pharmaceutical composition. Theinstructions relating to the use of the pharmaceutical compositiongenerally include information as to dosage, schedule and route ofadministration for the intended methods of use. In some embodiments, inwhich the kits comprise an antigen, the antigen may or may not bepackaged in the same container as the polynucleotide, linear chimericcompound or branched chimeric compound.

EXAMPLES

Abbreviations: BCC (branched chimeric compound); CC (chimeric compound);HEG (hexaethylene glycol); LCC (linear chimeric compound); MWCO(molecular weight cut-off); PEG (polyethylene glycol); PN(polynucleotide); Sp (spacer); TFF (tangential flow filtration).

Although, the present disclosure has been described in some detail byway of illustration and example for purposes of clarity andunderstanding, it will be apparent to those skilled in the art thatcertain changes and modifications may be practiced. Therefore, thefollowing synthetic and biological examples should not be construed aslimiting the scope of the present disclosure, which is delineated by theappended claims.

SYNTHETIC EXAMPLES Example 51 Structure of Polynucleotides and ChimericCompounds

Table S1-1 shows the structures of polynucleotides (PN) and chimericcompounds (CC) referred to in the Examples. The nucleotides in thepolynucleotides and chimeric compounds are 2′-deoxyribopolynucleotides.HEG is a hexaethylene glycol spacer moiety. Other spacers are describedin the specification and figures. Except where noted in Table 51-1 or inspecific examples, all internucleotide linkages and linkages betweennucleic acid moieties and spacer moieties are phosphorothioate esterlinkages. Table S1-1 also shows CCs (e.g., D56-02, D56-03, D56-07,D56-08, D56-10, D56-11) with an end linking group (e.g.,—(CH2)6-SS—(CH2)6-OH, —(CH2)6-SH, —(CH2)3SS—(CH2)3-OH, —(CH2)3SH,HO(CH2)6-SS—(CH2)6-, and HS(CH2)6-) used to link these molecules with abranched carrier moiety (e.g., [Maleimide-PEGn]y-FICOLL) to createbranched CCs. These linking groups are connected to the polynucleotideor CC via a terminal nucleotide or spacer moiety with a phosphorothioatelinkage. Branched CCs (e.g., [(D56-01)-PEGn]x-FICOLL) are prepared byconjugation strategies and have linking groups as described in theExamples.

TABLE S1-1Polynucleotide (PN) and Chimeric Compound (CC) Structures{circumflexover ( )} SEQ Cmpd. Cmpd. ID Number Nickname NO: Structure D56-01 N/A 25′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ D56-02 (D56-01)- 25′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′- 3′-SS(CH₂)₆-SS-(CH₂)₆-OH (see Example S2) D56-03 (D56-01)- 25′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′- 3′-SH(CH₂)₆-SH (see Example S3, Section F) D56-04 N/A 15′-TCGGCGC AACGTTC TCGGCGC-3′ D56-05 [(D56-01)- 2[(5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC- PEG₆]₈FIC3′-(CH₂)₆-S)-PEG₆-AECM]_(x)-FICOLL₄₀₀ (see Examples S3 and S9) D56-06N/A NA 5′-TCGACGT-3′ D56-07 (D56-06)- NA5′-TCGACGT-3′-HEG-(CH₂)₃-SS-(CH₂)₃-OH 3′-HEG-SS (see Example S2) D56-08(D56-06)- NA 5′-TCGACGT-3′-HEG-(CH₂)₃-SH 3′-HEG-SH (see Example S16)D56-09 [(D56-06)- NA[(5′-TCGACGT-3′-HEG-(CH₂)₃-S)-MC-AECM]_(x)-FICOLL₄₀₀ HEG-MC]_(x)-(see Example S16) FIC D56-10 1018 ISS 6 5′-TGACTGTGAA CGTTCGAGAT GA-3′D56-11 5′-SS- 6 HO(CH₂)₆SS(CH₂)₆-5′-TGACTGTGAA CGTTCGAGAT GA-3′ (D56-10)(see Example S2) D56-12 5′-HS- 6 HS(CH₂)₆-5′-TGACTGTGAA CGTTCGAGAT GA-3′(D56-10) (see Example S16) D56-13 [(D56-10)- 6FICOLL₄₀₀-[AECM-MC-(S(CH₂)₆-5′-TGACTGTGAA CGTTCGAGAT MC]_(x)-FICGA-3′)]_(x) (see Example S16) D56-14 N/A 75′-TCGTCGA-3′-HEG-5′-ACGTTCG-3′-HEG-5′-AGATGAT-3′ C56-15 N/A 85′-TCGACGT-3′-HEG-5′-TCGACGT-3′-HEG-5′-AACGTTC-3′ D56-16 N/A 95′-TCGTTCG-3′-HEG-5′-TCGTTCG-3′-HEG-5′-AACGTTC-3′ D56-17 N/A 105′-TCGTTCG-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGTTCG-3′ D56-18 N/A 115′-TCGGCGC-3′-HEG-5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ D56-19 N/A 125′-TCGCCGG-3′-HEG-5′-TCGCCGG-3′-HEG-5′-AACGTTC-3′ D56-20 N/A 135′-TCGCCGG-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGCCGG-3′ D56-21 N/A 145′-TCGATCG-3′-HEG-5′-TCGATCG-3′-HEG-5′-AACGTTC-3′ D56-22 N/A 155′-TCGTCGT-3′-HEG-5′-TCGTCGT-3′-HEG-5′-AACGTTC-3′ D56-23 N/A 165′-TCGTCGT-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGTCGT-3′ D56-24 N/A 175′-TCGACGT-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGACGT-3′ D56-25 [(D56-01)- 2[(5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC- PEG₂₄]_(x)-FIC3′-(CH₂)₆-S)-PEG₂₄-AECM]_(x)-FICOLL₄₀₀ (see Example S13) D56-26[(D56-01)- 2 [(5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-PEG₄₅]_(x)-FIC 3′-(CH₂)₆-S)-PEG₄₀-AECM]_(x)-FICOLL₄₀₀ (see Example S13)D56-27 [(D56-01)- 2 [(5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-PEG₇₀]_(x)-FIC 3′-(CH₂)₆-S)-PEG₇₀-AECM]_(x)-FICOLL₄₀₀ (see Example S13)D56-28 N/A 3 5′-TCGGCGC AACGTTC-3′ D56-29 N/A 45′-TCGGCGC-3′-HEG-5′-AACGTTC-3′ D56-30 Negative 55′-TGACTGTGAA CCTTAGAGAT GA-3′ Control {circumflex over ( )}Compoundsare given the same SEQ ID NO when the only difference from a compoundwith a defined SEQ ID NO is in non-nucleic acid moieties linked to the3′ nucleotide of D. Additionally, compounds having a nucleic acid moietycontaining fewer than 10 nucleotides are not assigned a SEQ ID NO andare therefore designated as NA (not applicable) above. FICOLL isabbrevaited as FIC.

Example S2 Synthesis of Polynucleotides (PN) and Chimeric Compounds (CC)

Polynucleotides were manufactured by solid phase synthesis usingphosphoramidite chemistry with oxidative sulfurization, purified andisolated according to the manufacturer's protocols (Molecules 2013, 18,14268-14284). The nucleoside monomers used were5′-dimethoxytrityl-protected-2′-deoxynucleoside,3′-((2-cyanoethyl)-(N,N-diisopropyl))-phosphoramidites. For the CCs, theHEG spacer was incorporated using18-O-dimethoxytritylhexaethyleneglycol,1-((2-cyanoethyl)-(N,N-isopropyl))-phosphoramidite (e.g., SpacePhorphoramidite 18 from Glen Research, Sterling, Va.). For D56-11, the5′-C6-disulfide linker was incorporated using1-O-dimethoxytrityl-hexyl-disulfide-1′-((2-cyanoethyl)-(N,N-diisopropyl))-phosphoramidite(e.g., Thiol-Modifier C6 S-S from Glen Research, Sterling, Va.). ForD56-07, the 3′-C3-disulfide linker was incorporated using1-O-dimethoxytrityl-propyl-disulfide, 1′-succinyl-solid support (e.g.,3′-Thiol-Modifier C3 S-S CPG from Glen Research, Sterling, Va.). ForD56-02, the 3′-C6-disulfide linker was incorporated using1-O-dimethoxytrityl-hexyl-disulfide, l′-succinyl-solid support (e.g.,3′-Thiol-Modifier C6 S-S CPG from Glen Research, Sterling, Va. or as acustom order from Prime Synthesis).

PN and CC were synthesized on a solid phase synthesizer programmed toadd the nucleotide monomers, HEG spacers and linkers in the desiredorder, with the synthesis occurring in the 3′ to 5′ direction. The3′-nucleoside or linker group (e.g., 3′-Thiol-Modifier C6 S-S CPG) wasattached to the solid support. The synthesis cycle consisted of adetritylation step using acid (e.g., dichloroacetic acid in toluene), acoupling step using the phosphoramidite monomer plus a mildly acidicactivator (e.g., saccharin 1-methylimidazole), an oxidativesulfurization step (e.g., 0.2 M Xanthane Hydride in pyridine), and acapping step for unreacted groups (e.g., isobutyric anhydride andN-methylimidazole). The synthesis cycle was repeated until the PN and CCsequence was fully assembled. The protected PN and CC were cleaved anddeprotected from the solid support (e.g., removal of cyanoethylphosphate protecting groups using 20% t-butylamine in acetonitrile,followed by treatment with concentrated aqueous ammonia to cleave PN orCC from support, and holding the resulting solution for 72 hours atambient temperature to remove the protecting groups on the nucleotides).The polynucleotides were purified using anion exchange chromatography,desalted by ultrafiltration/diafiltration using a tangential flowfiltration (TFF) system and lyophilized. PN and CC are stored frozen aslyophilized solids.

D56-02 was manufactured at the 10 mmol scale. The appearance was a whitepowder, the found molecular weight was 7780 (theoretical 7785 Da), thepurity by reverse phase HPLC was 85% and the purity by ion exchange HPLCwas 86%.

Alexa Fluor® 555-(D56-01) (aka fluorescently labeled D56-01) wasprepared by TriLink Biotechnologies (San Diego, Calif.). Alexa Fluor®brand fluorescent dyes are marketed by Molecular Probes, Inc. (Eugene,Oreg.).

Example S3 Manufacture of D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL

The D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) manufacturing scheme iscomprised of three stages, as shown in FIG. 1. Other PN or CC conjugatesto FICOLL can be prepared by the same manufacturing route by changingthe PN or CC sequence, the thiol linker to the PN or CC, and/or thethiol to amine crosslinker.

In Stage 1, FICOLL is modified in several steps to include a reactivemaleimide group, resulting in [Maleimide-PEG₆]_(y)-FICOLL. In Stage 2,the disulfide in D56-02 (aka (D56-01)-3′-SS) is reduced to a thiol,forming D56-03 (aka (D56-01)-3′-SH). In Stage 3,[Maleimide-PEG₆]_(y)-FICOLL and D56-03 react to form D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL). Purification occurs at each step in theprocess. The final D56-05 solution is sterile filtered andcharacterized. The D56-05 solution is stored at <−60° C.

FIG. 2 outlines the process for manufacture of the FICOLL intermediatescarboxymethylated (CM)-FICOLL, aminoethylcarbamylmethylated[AECM]_(z)-FICOLL, and [Maleimide (Mal)-PEG₆]_(y)-FICOLL, and the finalproduct D56-05, aka [(D56-01)-PEG₆]_(x)-FICOLL.

I. Composition of FICOLL PM400. FICOLL PM400 (FICOLL₄₀₀) is a syntheticneutral, highly-branched polymer of sucrose with a reported molecularweight of 400,000+/−100,000 that exists as a suspension ofnanoparticles. It is formed by copolymerization of sucrose withepichlorohydrin. FICOLL PM400 was purchased as a spray dried powder fromGE Healthcare (Pittsburgh, Pa.).

II. Stage 1, Step 1: Preparation of Carboxymethylated-FICOLL (CM-FICOLL)

CM-FICOLL was prepared from FICOLL PM400 by the method of Inman, J.Immunology, 1975, 114: 704-709) except that instead of using a standarddesalting procedure (e.g., dialysis using a 5 kDa molecular weightcut-off (MWCO) membrane), a purification using tangential flowfractionation (TFF) with a 100 kDa MWCO membrane was performed. The TFFpurification removed the small molecules and excess reagents similarlyto the standard desalting procedure.

CM-FICOLL is produced by reacting FICOLL PM400 with sodium chloroacetateunder basic conditions. The reaction scheme is shown FIG. 3. A solutionof FICOLL PM400 (13 g) was prepared at 130 mg/mL in Milli-Q deionizedwater. The solution was transferred to a jacketed reaction vesselconnected to a 40° C. circulating water bath, for 40-45 min. To thisFICOLL solution, 92.5 mL of 2.7 M sodium chloroacetate solution, 50 mLof 10 N sodium hydroxide solution, and 7.5 mL Milli-Q deionized waterwere added. The reaction proceeded for 2.5 hours at 40° C. whilestirring. Then, the reaction solution was transferred to a chilled glassbottle and placed on ice. Immediately thereafter, 10 mL of 2 M sodiumphosphate buffer pH 4 were added to the reaction solution, and the pHwas adjusted to 7.0 by addition of 20% chloroacetic acid solution. Thecrude CM-FICOLL was kept at low temperature (on ice) until ready forpurification. The crude CM-FICOLL was purified by diafiltration using asystem setup with a tangential flow fractionation (TFF) membrane havinga 100 kDa MWCO. The crude CM-FICOLL was diafiltered against 0.2 Maqueous sodium chloride for a total of approximately 15-18 volumeexchanges. The absorbance of each permeate diavolume was measured at 215nm and the diafiltration was stopped when the permeate absorbancereached 0.1 AU. The purified CM-FICOLL solution was concentrated toabout 30 mg/mL and stored at −80° C. Three lots of CM-FICOLL wereprepared by this process, each starting with 13 g of FICOLL PM400. Theyields of CM-FICOLL were 6.7 g, 7.1 g and 7.7 g.

III. Stage 1, Step 2: Preparation ofN-(2-aminoethyl)carbamylmethylated-FICOLL (aka [AECM]_(z)-FICOLL).[AECM]_(z)-FICOLL was prepared from CM-FICOLL by the method of Inman (J.Immunology, 1975, 114: 704-709) except that instead of using a standarddesalting procedure (e.g., dialysis using a 5 kDa molecular weightcut-off (MWCO) membrane), a purification using tangential flowfractionation (TFF) with a 100 kDa MWCO membrane was performed (asdescribed for CM-FICOLL in Section B).

[AECM]_(z)-FICOLL is produced by reacting CM-FICOLL with a large excessof ethylenediamine and a water soluble carbodiimide. The reaction schemeis shown FIG. 4. The CM-FICOLL solution (about 30 mg/mL in 0.2 M aqueoussodium chloride) was transferred to a jacketed reaction vessel connectedto a 22° C. circulating water bath for 20-30 min. To this CM-FICOLLsolution, ethylenediamine di-hydrochloride (approximately 13800 molarequivalent per FICOLL) was added, and completely dissolved. The pH ofthe solution was adjusted to 4.7 with 1 N aqueous sodium hydroxide.Then, N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride(EDC-HCl, approximately 835 molar equivalent per FICOLL) was added tothe mixture over a period of 10 min while stirring. The pH of thesolution was checked and if necessary adjusted to 4.7 with 1 N aqueoussodium hydroxide or 1 N aqueous hydrogen chloride. The reactionproceeded for 3.5 hours at 22° C. and during this time, the pH wasadjusted to 4.7, as required. The crude [AECM]_(z)-FICOLL was purifiedby diafiltration using a system setup with a tangential flowfractionation (TFF) membrane having a 100 kDa MWCO. The crude[AECM]_(z)-FICOLL was diafiltered against 100 mM sodium phosphate and150 mM sodium chloride, pH 7.5 buffer for a total of approximately 15-20volume exchanges. The absorbance of each permeate diavolume was measuredat 215 nm and the diafiltration was stopped when the permeate absorbancereached 0.1 AU. The purified [AECM]_(z)-FICOLL solution was concentratedto about 33 mg/mL, filtered using 0.22 μm pore size filter, aliquoted,and stored at −80° C. Three lots of [AECM]_(z)-FICOLL were prepared bythis process, starting with 6.5 g, 7.0 g and 7.5 g of CM-FICOLL. Theyields of [AECM]_(z)-FICOLL were 5.4 g, 5.9 g and 6.9 g, respectively.The amine to FICOLL molar ratios (z), determined using the proceduresdescribed in Example S4 and Example S5, were 221, 218 and 224,respectively.

IV. Composition of SM-PEG₆ Heterobifunctional Linker. SM-PEG₆(succinimidyl-((N-maleimidopropionamidol)-hexethyleneglycol) ester) wasobtained from Thermo Scientific (Catalog #22105 Rockford, Ill.). SM-PEG₆is an amine-to-sulfhydryl crosslinker with a molecular weight of 601.6containing a hydrophilic polyethylene glycol (PEG) spacer arm of sixethylene glycol units. The spacer arm length is about 32 angstroms. Thegeneral chemical structures of SM-PEG_(n) are shown in FIG. 5. ForSM-PEG₆, n=6 and the structure of the compound used was as shown in FIG.5A. For the preparation of D56-25, D56-26, and D56-27 in Example S13,SM-PEG_(n) with n=24, 45, and 70 were used, respectively.

V. Stage 1, Step 3: Preparation of [Maleimide-PEG₆]_(y)-FICOLL usingSM-PEG₆. [Maleimide-PEG₆]_(y)-FICOLL was prepared by reaction of[AECM]_(z)-FICOLL with SM-PEG₆. The reaction scheme is shown in FIG. 6.[AECM]_(z)-FICOLL solution (20 mg/mL in 100 mM sodium phosphate and 150mM sodium chloride, pH 7.5 buffer, amine to FICOLL molar ratio(z)=218-224) was transferred to a plastic bottle containing a stir bar.In a separate glass vial, SM-PEG₆ was dissolved in dimethylsulfoxide(DMSO) to a final concentration of 100 mg/mL solution. The SM-PEG₆solution (5 equivalents per amine) was added slowly to the[AECM]_(z)-FICOLL, while stirring. The reaction bottle was transferredto a 25° C. dry air incubator, and the reaction proceeded for 40 minwith gentle stirring. The reaction bottle was then transferred to roomtemperature (22-24° C.).

Unreacted amines on the FICOLL were capped usingsulfo-N-hydroxysuccinimidyl-acetate (Su-NHS-Ac, Thermo Scientific,Rockford, Ill.). Su-NHS-Ac was dissolved in DMSO in a glass vial to aconcentration of 100 mg/mL. The Su-NHS-Ac solution (5 equivalents peramine) was added to the [Maleimide-PEG₆]_(y)-FICOLL solution and wasstirred for 15 min at room temperature. This capping reaction convertsthe unreacted amines on the FICOLL to acetamides, which may be importantfor the physicochemical properties of the resulting FICOLL product.

Unreacted SM-PEG₆ and Su-NHS-Ac were quenched with glycine. Glycine wasdissolved in 100 mM sodium phosphate and 150 mM sodium chloride, pH 7.5buffer to a concentration of 100 mg/mL and the solution was filteredusing 0.22 μm pore size filter. The glycine solution (10 equivalents pertotal of SM-PEG₆ and Su-NHS-Ac) was added to the[Maleimide-PEG₆]_(y)-FICOLL solution and was stirred for 15 min at roomtemperature.

The [Maleimide-PEG₆]_(y)-FICOLL crude preparation was kept at lowtemperature (on wet ice) until ready for purification, which wasperformed on the same day as the conjugation reaction. The crude[Maleimide-PEG₆]_(y)-FICOLL was purified by diafiltration using a systemsetup with a tangential flow fractionation (TFF) membrane having a 100kDa MWCO. The crude [Maleimide-PEG₆]_(y)-FICOLL was diluted to about 5.8mg/mL using 100 mM sodium phosphate, 150 mM sodium chloride, pH 7.5buffer, and was diafiltered against 100 mM sodium phosphate, 150 mMsodium chloride, pH 7.5 buffer for a total of approximately 24-29 volumeexchanges. The absorbance of each permeate diavolume was measured at 215nm and the diafiltration was stopped when the permeate absorbancereached 0.1 AU. The purified [Maleimide-PEG₆]_(y)-FICOLL was aliquotedinto sterile polypropylene vials and stored at −80° C. The concentrationwas about 5.3 mg/mL. For the two largest scale reactions (Pilot Lots 4and 5), 655 mg and 1900 mg of [AECM]_(z)-FICOLL were used and 444 mg and1288 mg of purified [Maleimide-PEG₆]_(y)-FICOLL were isolated.

The maleimide to FICOLL molar ratio (y) of [Maleimide-PEG₆]_(y)-FICOLLwas determined by the procedures outlined in Example S4 and Example S6.Table S3-1 shows the consistency of the [Maleimide-PEG₆]_(y)-FICOLLproduced using three different lots of [AECM]_(z)-FICOLL, two differentlots of SM-PEG₆ linker, and two different scales of production.Production of [Maleimide-PEG₆]_(y)-FICOLL having a specified range ofmaleimide:FICOLL molar ratios (y about 162-221) requires control of thefollowing reagents and process parameters: 1) preparation of[AECM]-FICOLL with an amine:FICOLL molar ratio (z) of about 218-224, 2)having highly pure SM-PEG₆ linker, 3) and defined reaction conditionsfor reagent concentrations, stoichiometry, ionic strength, pH, time andtemperature.

TABLE S3-1 Consistent Production of [Maleimide-PEG₆]_(y)-FICOLL at Benchand Pilot Scales Using Three Different Lots of [AECM]_(z)-FICOLL and TwoDifferent Lots of SM-PEG₆ [Maleimide- SM-PEG₆ PEG₆]_(y)-FICOLL linkerAmine:FICOLL Maleimide:FICOLL Lot No. Lot No. molar ratio (z) molarratio (y) Bench Lot 1 Lot A 218 (Lot 2) 174 Bench Lot 2 Lot A 218 (Lot2) 162 Bench Lot 3 Lot A 218 (Lot 2) 176 Bench Lot 4 Lot A 218 (Lot 2)181 Pilot Lot 1 Lot A 221 (Lot 1) 163 Pilot Lot 2 Lot A 218 (Lot 2) 182Pilot Lot 3 Lot A 224 (Lot 3) 187 Pilot Lot 4 Lot B 224 (Lot 3) 221Pilot Lot 5 Lot B 224 (Lot 3) 206

The purity of [Maleimide-PEG₆]_(y)-FICOLL Pilots Lots 4 and 5 wasassessed by size exclusion chromatography—high performance liquidchromatography (SEC-HPLC) using the parameters shown in Table S3-2. Thechromatograms for crude and purified Pilot Lots 4 and 5 are shown inFIG. 7. Purified Pilot Lots 4 and 5 were 100% and 99.6% pure,respectively.

TABLE S3-2 SEC-HPLC Method For Purity Determination Column TOSOH TSK-GelG3000 PW_(XL) Dimensions 7.8 mm × 30 cm Bed Volume 14.3 ml Flow Rate0.75 ml/min Mobile Phase 10 mM sodium phosphate, 141.7 mM sodiumchloride, pH 7.2 buffer Run Time 20 min Detection UV at 215 and 260 nmInjection Volume 20 μl

The [Maleimide-PEG₆]_(y)-FICOLL manufactured using the SM-PEG₆ linkerwas significantly more soluble in aqueous buffers than[Maleimide-MC]_(y)-FICOLL manufactured using the sulfosuccinimidyl4-(N-maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC) linker,which was previously described in U.S. Pat. No. 8,597,665. Thesulfo-SMCC linker results in a hydrophobic methylcyclohexyl (MC) linkinggroup, which causes the [Maleimide-MC]_(y)-FICOLL to oil out and/orprecipitate in aqueous buffers after freeze/thaw cycle(s), and resultsin unreliable reaction with the thiol-activated polynucleotide (PN) orchimeric compound (CC). If the [Maleimide-PEG₆]_(y)-FICOLL or[Maleimide-MC]_(y)-FICOLL are not used on the day they are prepared,they must be stored frozen so that the maleimide group remains active.The heterogeneous mixtures of [Maleimide-MC]_(y)-FICOLL were not used inconjugation reactions with D56-03 (aka (D56-01)-3′-SH) due to their poorstability. Refer to Example S14 for the synthesis of[Maleimide-MC]_(y)-FICOLL.

F. Stage 2, Step 1: Preparation of D56-03 (aka (D56-01)-3′-SH). D56-03(thiol) was prepared by reaction of D56-02 (disulfide) with excesstris(2-carboxyethyl)phosphine hydrochloride (TCEP). The reaction schemeis shown in FIG. 8. On the day of production, D56-02 (aka(D56-01)-3′-SS) was removed from the freezer and allowed to equilibrateto room temperature for at least 1-2 hours before opening the bottle tominimize water uptake in the hygroscopic lyophilized solid. D56-02 wasdissolved in activation buffer (100 mM sodium phosphate, 150 mM sodiumchloride, 1 mM ethylenediaminetetraacetic acid (EDTA), pH 7.5) to anominal concentration of about 56 mg/mL. The actual concentration of thesolution was determined by absorbance at 260 nm using an extinctioncoefficient of 22.65 mg/mL⁻¹ cm⁻¹. The concentration was adjusted toapproximately 25 mg/ml with activation buffer, and verified byabsorbance at 260 nm.

TCEP-HCl was obtained from Thermo Scientific (Catalog #20490, Rockford,Ill.). On the day of production, TCEP-HCl was dissolved in activationbuffer to a concentration of 48±1 mg/mL. The TCEP solution was kept atambient lab temperature and used within 3 hours.

To the D56-02 solution, TCEP solution (5 equivalents) was added at roomtemperature with stirring. The reaction vessel was transferred to a40±2° C. water bath, and the reduction step proceeded for 120±10 min.The resulting crude D56-03 solution was allowed to cool to roomtemperature for about 10-15 min prior to purification. This reaction wasperformed on 989 mg of D56-02 for Pilot Lot 4 and in two parts on 1814mg and 1836 mg of D56-02 for Pilot Lot 5.

Purification of D56-03 was achieved by gel filtration using SephadexG-25 Fine (Catalog #17-0032, GE Healthcare, Pittsburgh, Pa.) packed intoXK50/30 columns (GE Healthcare) according to the manufacturer'srecommended procedures. The G25 desalting chromatography columns werecontrolled by an AKTA purifier chromatography system, (GE Healthcare,formerly Amersham Pharmacia Biotech). The crude D56-03 solution wasloaded onto the G25 column at a ratio of 15-16% of sample volume tocolumn volume. The mobile phase was applied to the column at a flow rateof 30 cm/hr. The eluent from the column was monitored at 215 nm and 260nm, and sample collection started when eluent absorbance rose aboveapproximately 100 mAU. A total volume of about 1.6 to 1.7 times thesample volume loaded on the column was collected. The purified D56-03solutions were aliquoted and stored at −80° C. Details of thepurification of Pilot Lots 4 and 5 are detailed in Table S3-3.

TABLE S3-3 Purification of D56-03 Pilot Lots 4 and 5 D56-03 Pilot D56-03Pilot Lot 5 Step Lot 4 Part 1 Part 2 Crude Sample volume 41 mL 77 mL 78mL D56-03 Sample amount 984 mg 1874 mg 1833 mg Gel Sephadex G-25 bedsize 5 × 13 cm 5 × 26 cm 5 × 26 cm Filtration (Diameter × Height)Sephadex G-25 column 255 mL 510 mL 510 mL volume Mobile phase 100 mMsodium phosphate, 150 mM sodium chloride, 1 mM EDTA, pH 7.5 bufferOperating flow rate 30 cm/hr 30 cm/hr 30 cm/hr 9.8 ml/min 9.8 ml/min 9.8ml/min Sample volume to 16% 15% 15% column volume ratio Temperature RT(22-24° C.) RT (22-24° C.) RT (22-24° C.) Column back pressure Notrecorded 0.16 MPa 0.19 MPa Purified D56-03 pool volume 70 mL 127 mL 128mL D56-03 collected Pool volume to sample 1.7 1.6 1.6 volume ratio

The purity of D56-03 was determined by SEC-HPLC using the procedureoutlined in Table S3-2 and was 100% for Pilot Lots 4 and 5 (FIG. 9). ForPilot Lots 4 and 5, 802 mg and 2904 mg of D56-03 were isolated,respectively.

G. Stage 3, Step 1: Preparation of D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL. D56-05 was prepared by reaction of[Maleimide-PEG₆]_(y)-FICOLL with D56-03 (aka (D56-01)-3′-SH). Thereaction scheme is shown in FIG. 10.

Both [Maleimide-PEG₆]_(y)-FICOLL and D56-03 are reactive and must behandled with care. Both materials were stored frozen at −80° C. and werethawed in a 4° C. water bath for several hours just prior to use. The[Maleimide-PEG₆]_(y)-FICOLL solution (about 5.3 mg/mL, maleimide:FICOLLmolar ratio (y)=206-221) was transferred to a plastic bottle containinga stir bar. To this solution, a solution of D56-03 (about 11.5 mg/mL,0.64-0.69 equivalents per maleimide, 141 equivalents per FICOLL) wasadded while stirring. The volume in the reaction vessel was adjustedwith 100 mM sodium phosphate, 150 mM sodium chloride, pH 7.5 in order toobtain a final D56-03 concentration of 5 mg/mL. The conjugation reactionwas then transferred to a 25° C. dry air incubator, and the reactionproceeded for 1 hour with gentle stirring. For Pilot Lot 4, 218 mg of[Maleimide-PEG₆]_(y)-FICOLL and 600 mg of D56-03 were used. For PilotLot 5, 874 mg of [Maleimide-PEG₆]_(y)-FICOLL and 2400 mg of D56-03 wereused.

Unreacted maleimide groups on the FICOLL were capped for 15 min at roomtemperature using a 100 mg/mL solution of cysteine in 100 mM sodiumphosphate, 150 mM sodium chloride, pH 7.5 buffer (10 equivalents permaleimide). The crude [(D56-01)-PEG₆]_(x)-FICOLL was then transferred tothe cold room (2-8° C.), and stored overnight. This capping reactionintroduces cysteine onto the FICOLL (via a covalent bond through thesulfur), and may be important for the physicochemical properties of theD56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) product.

Purification of D56-05 was performed by diafiltration, as described inTable S3-4. The volume of crude D56-05 was adjusted with 10 mM sodiumphosphate, 142 mM sodium chloride, pH 7.2 buffer. At each diavolume (avolume of permeate equal to the starting sample volume in the feedreservoir), a sample of permeate was taken to determine the absorbanceat 215 nm. Diafiltration was ended when the permeate absorbance droppedbelow 0.05 AU. Upon completion of diafiltration, the D56-05 sample wasrecovered from TFF system and sterile filtered using a 0.22 μm filter.The D56-05 was aliquoted and stored at <−60° C. D56-05 pilot lots werecharacterized and the results are provided in Example S9.

TABLE S3-4 Parameters and Conditions for Diafiltration of D56-05 PilotLots 4 and 5 Step D56-05 Pilot 4 D56-05 Pilot 5 Crude Sample volume 121mL 485 mL D56-05 Sample amount 593 mg 2386 mg Final sample volume 200 mL600 mL after adjustment D56-05 Membrane surface area 0.1 m² 0.2 m²Diafiltration Buffer 10 mM sodium phosphate, 142 mM sodium chloride, pH7.2 buffer Tubing Size LS/16 LS/15 Pump Speed 150-160 mL/min 200 mL/minAverage Permeate 50 mL/min 67 mL/min Flow Rate Temperature (22-24° C.)(22-24° C.) Transmembrane 1 to 8 psi 2.2 to 9.8 psi pressure TotalBuffer 6.2 liters 14 liters Number of buffer 31 diavolumes^(a) 23diavolumes^(a) exchanges Duration 3.3 hours 3.5 hours Permeateabsorbance at 0.028 AU 0.036 AU 215 nm at end of diafiltration PurifiedVolume 130 mL ~375 mL^(b) D56-05 ^(a)Diavolume is the volume of permeateequivalent to the sample volume in the feed reservoir. Each diavolume isone buffer exchange. ^(b)Volume of D56-05 Pilot 5 after diafiltrationwas an approximation. An actual volume measurement was not performed.

Example S4 Procedure to Determine FICOLL Concentration inFICOLL-Containing Intermediates and Products

The FICOLL concentrations of FICOLL-containing intermediates andproducts were determined using the Pierce Glycoprotein CarbohydrateEstimation Kit (Product #23260, Thermo Scientific, Rockford, Ill.) asper the manufacturer's protocol, except that FICOLL PM400 was used tocreate a standard curve for the assay.

Example S5 Procedure to Determine Amine Concentration and Amine:FICOLLMolar Ratio (z) in [AECM]_(z)-FICOLL Solutions

The amine concentration of [AECM]_(z)-FICOLL was determined using thePierce Fluoraldehyde OPA Reagent Solution (Product #26025, ThermoScientific, Rockford, Ill.) as per the manufacturer's protocol. Glycinewas used to create a standard curve for the assay. The Amine:FICOLLmolar ratio (z) was calculated by dividing the amine concentration bythe FICOLL concentration, where the FICOLL concentration was determinedas described in Example S4 and the concentrations were in units ofmolarity.

Example S6 Procedure to Determine Maleimide Concentration andMaleimide:FICOLL Molar Ratio (y) in [Maleimide]_(y)-FICOLL Solutions

The maleimide concentrations of [Maleimide-PEG₆]_(y)-FICOLL and[Maleimide-MC]_(y)-FICOLL were determined using Ellman's reagent(5,5′-dithio-bis-(2-nitrobenzoic acid), Product No. 22582, ThermoScientific, Rockford, Ill.). The [Maleimide]_(y)-FICOLL was reacted withexcess cysteine as per the manufacturer's protocol, and the remainingcysteine was quantified using a cysteine standard curve. The maleimideconcentration was determined by subtracting the remaining cysteineconcentration from the initial cysteine concentration. TheMaleimide:FICOLL molar ratio (y) was calculated by dividing themaleimide concentration by the FICOLL concentration, where the FICOLLconcentration was determined as described in Example S4 and theconcentrations were in units of molarity.

Example S7 Procedure to Determine Polynucleotide (PN) or ChimericCompound (CC) Concentration and PN:FICOLL or CC:FICOLL Molar Ratio (x)in FICOLL Conjugates (e.g., D56-05, aka [(D56-01)-PEG₆]_(x)-FICOLL)

The D56-01 (CC) concentration of D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL)was determined using ultraviolet spectrophotometry and the Beer's lawequation. (Note that by convention, the chimeric compound attached tothe FICOLL is referred to by the sequence name, D56-01, at this stageeven though the chimeric compound with the linker, D56-03, was used toform this compound.) The absorbance at 260 nm was determined and anextinction coefficient of 22.65 mg/ml⁻¹×cm⁻¹ for D56-01 was used. FICOLLand the linkers do not absorb at 260 nm, so the absorbance is solely dueto the absorbance of the CC, D56-01. The D56-01 concentration in mg/mLwas converted to a molar concentration using the molecular weight of thefree acid for D56-01. The CC:FICOLL molar ratio (x) was determined bydividing the CC concentration by the FICOLL concentration, where theFICOLL concentration was determined as described in Example S4 and theconcentrations were in units of molarity. Concentrations for otherPN-FICOLL or CC-FICOLL solutions are determined using the extinctioncoefficient and free acid molecular weight for the PN or CC used, asappropriate.

Example S8 Procedure to Determine Particle Size

The particle sizes (Z-average) and standard deviations (SD) of FICOLLsamples (e.g., D56-05) were measured by dynamic light scattering (DLS)using a Malvern Zetasizer instrument. Samples were diluted to a FICOLLconcentration of 0.5 mg/mL in 10 mM sodium phosphate, 142 mM sodiumchloride, pH 7.2 buffer, and measured under defined instrument settings.A calibrated 50 nm polystyrene nanosphere sample (Product #3050A, ThermoScientific, Rockford, Ill.) was included in the analysis as a systemsuitability control and had had a particle size of 49±6 nm.

Example S9 Physicochemical Characterization of Purified D56-05, Aka[(D56-01)-PEG₆]_(x)-FICOLL

Five pilot lots of D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) have beenmanufactured using the procedure outlined in Example S3. These lots werecharacterized and the results are summarized in Table S9-1. Purity wasdetermined by SEC-HPLC using the procedure outlined in Table S3-2 withdetection at 215 nm and ranged from >99% to 100%. FICOLL concentrationwas determined by the procedure described in Example S4. The FICOLLconcentration can be targeted by controlling the final concentration ofthe retentate in the diafiltration. D56-01 concentration and theD56-01:FICOLL ratio (x) were determined by the procedure described inExample S7. The D56-01:FICOLL molar ratio (x) ranged from 117 to 140,demonstrating that the manufacturing procedure described in Example S3provides a high level of control for the loading of the chimericcompound on the FICOLL. The target D56-01:FICOLL molar ratio (x) forthis process is 120±30. The particle size of D56-05 was determined asdescribed in Example S8.

TABLE S9-1 Summary of the Physical Characterization of Purified D56-05Pilot Lots Attribute Pilot 1 Pilot 2 Pilot 3 Pilot 4 Pilot 5Appearance^(a) Clear liquid Clear liquid Clear liquid Clear liquid Clearliquid pH 7.3 7.2 7.1 7.2 7.2 Purity (area %)^(b) >99%  >99%  >99   100%  100%  Residual D56-03 (area %)^(b) <1%  <1%  <1%  0% 0% FICOLLconcentration 1.3 1.2 1.3 1.6 2.3 (mg/mL)^(c) D56-01 concentration 2.93.2 3.0 3.8 5.7 (mg/mL)^(d) D56-01:FICOLL 117    140    117    126   125    molar ratio (x) Particle size (nm): 49 ± 20 53 ± 23 47 ± 20 47 ±20 48 ± 20 Z-average ± SD^(e) ^(a)Appearance was determined by visualevaluation. ^(b)Purity and residual D56-03 (aka (D56-01)-3′-SH) wasdetermined using an SEC-HPLC silica-based column using the parameters inTable S3-2 with detection at 215 nm. ^(c)FICOLL concentrations weredetermined as described in Example S4. ^(d)D56-01 concentrations andD5601:FICOLL molar ratios (x) were determined as described in ExampleS7. ^(e)Mean particle diameter was determined as described in ExampleS8.

The results shown in Table S9-1 illustrate the consistency of productionof five consecutively-produced pilot lots of D56-05. This high level ofcontrol for the key attributes D56-01:FICOLL molar ratio (x) andparticle size of D56-05 was achieved by using the reagents andprocedures outlined in Example S3. Use of the SM-PEG₆ linker instead ofthe sulfo-SMCC linker to manufacture the [Maleimide]_(y)-FICOLL wascritical, as the SM-PEG₆ linker made the product significantly morewater soluble leading to improved control of the maleimide:FICOLL molarratio (y) and reactivity with D56-03. Additionally, the quality (purity)of the reagents and control of process parameters, including number ofequivalents, concentrations, pH, ionic strength, time, and temperature(as described in Example S3), were critical for achieving consistentresults. Development of the analytical procedures described in ExamplesS4-S8 were also necessary for control of the process.

Example S10 D56-05 Lyophilized Formulation

Limitations in the stability of D56-05 solution formulations storedabove 5° C. led to development of a D56-05 lyophilized formulation, withthe goal of achieving good stability at controlled room temperature (seeExample S11). Selection of the composition of the formulation to belyophilized was based upon pre-formulation studies using GenerallyRegarded as Safe (GRAS) excipients to control pH and ionic strength,which can affect thermal stability. A series of test formulations basedupon D56-05 primate dosages were tested for freeze/thaw stability andevaluated on the basis of solution clarity and HPLC sizingchromatography. A formulation containing 1 mg/ml D56-05 (Pilot Lot 2),10 mM potassium phosphate (pH=7.5) and 300 mM trehalose showed identicalchromatographic behavior and dynamic light scattering profiles throughthe 10-cycle experiment and was selected for further development. Theformulation described above was subjected to a lyophilization cycle,consisting of shelf-freezing at approximately −35° C., followed by 36hours of primary drying at −35° C. (˜60 Oar vacuum), 2-hour transitionto shelf temperature at 30° C., and secondary drying for an additional24 hours. The lyophilized product (40 vials) was an acceptable cakeshown to have residual moisture of 1-1.4%. The formulation wasreconstituted in 1 mL of water and the product was shown to behaveidentically by SEC-HPLC when analyzed directly after formulation orafter the lyophilization and reconstitution process.

Example S11 Stability of D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL)Solution and Lyophilized Formulations

This example describes the stability of liquid and lyophilizedsubstances.

A. D56-05 Solution Formulation Stability. The stability of the D56-05(aka [(D56-01)-PEG₆]_(x)-FICOLL) solution formulation over 12 months ofstorage was evaluated. The solution formulation consisted of D56-05dissolved in 10 mM sodium phosphate, 142 mM sodium chloride, pH 7.2buffer at concentrations of about 3-5 mg/mL. The stability of D56-05solution formulation (Pilot Lot 4) was evaluated at storage temperaturesof −80° C., 5° C. and 37° C. The stability tests included pH, D56-01concentration (Example S7), % purity of D56-05 by SEC-HPLC (Table S3-2,detection at 215 nm) and particle size analysis (Example S8).

Table S11-1 and Table S11-2 show the stability results for D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) solution formulation, Pilot Lot 4, stored at−80° C., 5° C. and 37° C. for up to 12 months. The time 0 results areshown in Table S9-1.

TABLE S11-1 Stability Results for D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) Solution Formulation, Pilot Lot 4 TestD56-01 Concentration % Purity of D56-05 by pH (mg/mL) SEC-HPLC, area%^(a) Time Sample Months Months Months Temp. 3 6 9 12 3 6 9 12 1 3 6 912 −80° C. 7.3 7.3 7.3 7.3 3.6 3.6 3.6 3.4 98.9 99.6 100 99.6 99.6  5°C. 7.2 7.2 7.2 7.1 3.7 3.7 3.8 3.4 99.0 99.5 98.3 98.1 97.8   37° C.^(b)7.0 6.5 6.4 N/A 3.9 N/A N/A N/A 93.4 89.0 79.1 77.4 N/A ^(a)A polymercolumn (TSK-Gel G3000PW_(XL)) was used to test the 1-month stabilitysamples. A silica column (TSK-Gel G3000SW_(XL)) was used to test the 3,6, 9 and 12-month stability time-point samples. Purity determined at 215nm. ^(b)Some samples stored at 37° C. were compromised due to crack incap to tube and thus were not analyzed. These samples are reported asN/A (data not available).

TABLE S11-2 Particle Size Distribution of D56-05 (aka[(D56-01)-PEG₆]_(x)- FICOLL) Solution Formulation, Pilot Lot 4 StabilitySamples Time Point Storage Temperature Intensity 1-Month  −80° C.  45.9± 22.9 nm  5° C. 45.9 ± 22.5 nm 37° C. 44.9 ± 21.6 nm 3-Months −80° C. 54.3 ± 27.5 nm  5° C. 58.6 ± 28.9 nm 37° C. 62.4 ± 30.5 nm 6-Months −80°C.  49.8 ± 23.1 nm  5° C. 52.7 ± 27.5 nm 37° C. 47.3 ± 22.4 nm 9-Months−80° C.  49.8 ± 21.6 nm  5° C. 49.3 ± 20.6 nm 37° C. 45.2 ± 19.9 nm12-Months  −80° C.  49.0 ± 21 nm  5° C. 48.7 ± 21 nm 37° C. Notavailable

For the D56-05 solution formulation, Pilot Lot 4, the pH, D56-01concentration, D56-05 purity and particle size did not changesignificantly with storage at frozen (−80° C.) or refrigerated (5° C.)conditions for up to 12 months. However, at 37° C., both pH and D56-05purity decreased significantly with longer storage times, while D56-01concentration and particle size remained consistent. The consistency ofthe D56-05 particle size under the different storage conditions showsthat D56-05 does not aggregate over time.

B. D56-05 Lyophilized Formulation Stability. The stability of the D56-05(aka [(D56-01)-PEG₆]_(x)-FICOLL) lyophilized formulation over 12 monthsof storage was evaluated. The lyophilized formulation is described inExample S10. The stability of D56-05 lyophilized formulation wasevaluated at storage temperatures of 4° C., 25° C. and 37° C. Thestability tests included pH, D56-01 concentration (Example S7), % purityof D56-05 by SEC-HPLC (Table S3-2 with detection at 215 nm) and particlesize analysis (Example S8).

Table S11-3 shows the stability results for the D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) lyophilized formulation stored at 4° C., 25°C. and 37° C. for up to 12 months. Data for the D56-05 formulationbefore lyophilization (pre-lyo) is also included in Table S11-3.

TABLE S11-3 Stability Results for D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) Lyophilized Formulation (Formulation inExample S10) Pre- 1 Month 6 Months 12 Months Test lyo T₀ 4° C. 25° C.37° C. 4° C. 25° C. 37° C. 4° C. 25° C. 37° C. pH 7.5 7.4 7.5 7.5 7.57.6 7.5 7.6 7.5 7.5 7.4 [D56-01] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.01.0 (mg/mL) Purity 99.5 99.5 99.4 99.4 99.5 100 100 100 99.6 99.7 99.5(area %) Particle 35 ± 16 28 ± 17 27 ± 17 28 ± 20 34 ± 23 28 ± 18 48 ±35 67 ± 47 28 ± 18 50 ± 35 217 ± 159 size^(b) (nm)

For the D56-05 lyophilized formulation, the pH, D56-01 concentration,and D56-05 purity did not change significantly with storage at 4° C.,25° C. and 37° C. for up to 12 months. The particle size was also stablewith storage at 4° C. for up to 12 months. However, a minor increase inparticle size was observed for product stored at 25° C. for 12 months,while a large increase in particle size (about 6×) was evident forsamples stored at 37° C. for 12 months. However, in vitro biologicalactivity (human B-cell IL-6 production) was unchanged after 12 monthsstorage at any temperature. It was concluded that the lyophilizedformulation is sufficiently stable for at least 12 months at 25° C.

Although the D56-05 solution formulation is stable at frozen (−80° C.)and refrigerated (5° C.) storage conditions, the D56-05 lyophilizedformulation displayed enhanced stability compared with D56-05 insolution, especially at higher storage temperatures of 25° C. and 37° C.

Example S12 Preparation of [Maleimide-PEG₆]_(y)-FICOLL with DifferentMaleimide:FICOLL Molar Ratios (y), and Impact on D56-01:FICOLL MolarRatio (x) in Purified D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL)

[Maleimide-PEG₆]_(y)-FICOLL lots with different maleimide:FICOLL molarratios (y) were produced from (AECM)_(z)-FICOLL (amine:FICOLL molarratio (z)=224) using the procedure described in Example S3, Section Eexcept at smaller scale and using different amounts of SM-PEG₆ (0.25,0.5, 0.75, 1.0, & 2.0 equivalents per amine). The maleimide:FICOLL molarratios (y) were determined by the procedures described in Examples S4and S6. The results in Table S12-1 show that adding different amounts ofSM-PEG₆ resulted in [Maleimide-PEG₆]_(y)-FICOLL lots withmaleimide:FICOLL molar ratios (y) from 8 to 185. The[Maleimide-PEG₆]_(y)-FICOLL lots were then reacted with D56-03 (1.1equivalent per maleimide) and the resulting D56-05 lots were purified asdescribed in Example S3, Section G. The D56-01:FICOLL molar ratios (x)of the D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) lots were determined asdescribed in Examples S4 and S7, and ranged from 24-154 (Table S12-1).These results show that the D56-01 loading in D56-05 can be controlledby the amount of SM-PEG₆ used in the preparation of[Maleimide-PEG₆]_(y)-FICOLL. See Example B9 for the in vitro potency ofthese compounds.

TABLE S12-1 Summary of Preparation of [Maleimide-PEG₆]_(y)-FICOLL Lotswith Different Maleimide:FICOLL Ratios (y), and Effect on D56-01 MolarRatios (x) in D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) Test 1 Test 2 Test3 Test 4 Test 5 Test 6 Equivalents SM-PEG₆ per 0.25 0.5 0.75 1.0 1.5 2.0amine Maleimide:FICOLL ratio (y) in 8 28 61 101 176 185[Maleimide-PEG₆]_(y)-FICOLL Equivalents of D56-03 per ND 1.1 1.1 1.10.75 1.1 maleimide in [Maleimide- PEG₆]_(y)-FICOLL D56-01:FICOLL molarratio (x) ND 24 53 82 124 154 in D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL) ND = Not done.

Example S13 Preparation of D56-25, D56-26 and D56-27 (aka[(D56-01)-PEG_(n)]_(x)-FICOLL) using SM-PEG_(n) Linkers with n=24, 45,and 70, Respectively

[Maleimide-PEG_(n)]_(y)-FICOLL lots with different PEG linker lengthswere produced from (AECM)_(z)-FICOLL (amine:FICOLL molar ratio (z)=224)using the procedure described in Example S3, Section E, except atsmaller scale and using SM-PEG_(n) linkers with n=24, 45, and 70,respectively (see FIG. 5 for chemical structures of SM-PEG_(n)). TheSM-PEG₂₄ reagent used was obtained from Thermo Fisher (Rockford, Ill.),which has the structure as shown in FIG. 5-A where n is 24. The SM-PEG₄₅and SM-PEG₇₀ reagents used were obtained from Nanocs Inc., (New York,N.Y.); and the structures are as shown in FIG. 5-B (n is 45 and 70respectively). The maleimide:FICOLL molar ratios (y) of the resulting[Maleimide-PEG₆]_(y)-FICOLL lots were determined as described inExamples S4 and S6 and the results are shown in Table S13-1. Themaleimide:FICOLL molar ratios (y) ranged from 199 to 227, showing thatthe PEG linker length did not significantly affect the maleimide:FICOLLmolar ratios obtained.

D56-25, D56-26 and D56-27 (aka [(D56-01)-PEG_(n)]_(x)-FICOLL with n=24,45 and 70, respectively) were prepared from the three[Maleimide-PEG_(n)]_(y)-FICOLL lots as described in Example S3, SectionG except on a smaller scale. The D56-01:FICOLL molar ratios (x) of the[(D56-01)-PEG_(n)]_(x)-FICOLL lots (D56-05 (n=6), D56-25 (n=24), D56-26(n=45) and D56-27 (n=70)) were determined as described in Examples S4and S7 and the mean particle diameter was determined as described inExample S8. The D56-01:FICOLL molar ratios (x) ranged from 108 to 116(Table S13-1), showing that the PEG linker length did not significantlyaffect the D56-01:FICOLL molar ratios obtained. However, there was anincrease in mean particle diameter (from 55 nm to 91 nm) that correlatedwith increase length of the PEG linker (Table S13-1). See Example B10for the in vitro potency of these compounds.

TABLE S13-1 Effects of SM-PEG_(n) Linker Length on[(D56-01)-PEG_(n)]_(x)-FICOLL Properties D56-05 D56-25 D56-26 D56-27PEG_(n) length (n)  6  24  45  70 Maleimide:FICOLL molar ratio (y) 215199 227 225 in [Maleimide-PEG_(n)]_(y)-FICOLL D56-01:FICOLL molar ratio(x) in 109 116 110 108 [(D56-01)-PEG_(n)]_(x)-FICOLL Purity   >99%  >99%   >99%   >99% Mean particle diameter (nm)^(a) 55 nm 77 nm 78 nm91 nm ^(a)Mean particle diameter was determined as described in ExampleS8.

Example S14 Preparation of [Maleimide-MC]_(y)-FICOLL

[Maleimide-MC]_(y)-FICOLL was manufactured from [AECM]_(z)-FICOLL usingthe sulfo-SMCC linker as described U.S. Pat. No. 8,597,665.[Maleimide-MC]_(y)-FICOLL showed solubility problems in aqueous buffers,observed as oiling out and/or precipitation. The difficulty in handlingthe Maleimide-MC-FICOLL made conjugation reactions with thiol-activatedpolynucleotide (PN) or chimeric compound (CC) inconsistent.

Example S15 Preparation of Alexa Fluor® 555-(D56-05) (aka Alexa Fluor®5551[(D56-01)-PEG₆]_(x)-FICOLL)

The amine reactive derivative of Alexa Fluor® 555 (Alexa Fluor® 555-NHSester) was purchased from Life Technologies (Foster City, Calif.).AECM-FICOLL, prepared as described in Example S3, was activated byreaction with a mixture of Alexa Fluor® 555-NHS Ester and SM-PEG₆ toform Alexa Fluor® 555/[Maleimide-PEG₆]_(y)-FICOLL which was reacted withD56-03 (aka (D56-01)-3′-SH) as described in Example S3 to yield AlexaFluor® 555-(D56-05) (aka Alexa Fluor® 555/[(D56-01)-PEG₆]_(x)-FICOLL).

Example S16 Preparation of D56-08, D56-09, D56-12 and D56-13

D56-08, D56-09, D56-12 and D56-13 are prepared as described in U.S. Pat.No. 8,597,665.

Example S17 Preparation of Alexa Fluor® 647-(D56-05) (aka Alexa Fluor®6471[(D56-01)-PEG₆]_(x)-FICOLL)

Fluor 647-NHS ester (Life Technologies) was reacted with rPA to yieldAlexa Fluor® 647/rPA with a resulting ratio of one Alexa Fluor® 647 perrPA.

BIOLOGICAL EXAMPLES Example B1 Isolation and Stimulation of HumanLeukocytes

Activity of polynucleotides (PN) and chimeric compounds (CC) wereassessed in vitro by measurement of cytokine secretion by humanperipheral blood mononuclear cells (PBMC) and isolated B cells, as wellas by measurement of B cell proliferation. Cytokine levels secreted intocell culture media were measured by enzyme-linked immunosorbent assay(ELISA).

Human blood was obtained with informed consent from healthy humandonors. PBMC were isolated by FICOLL-Paque (GE Healthcare, UK) densitygradient centrifugation. Human B cells were isolated by positiveselection with anti-CD19 microbeads (Miltenyi Biotec, Auburn, Calif.).Human plasmacytoid dendritic cells (pDCs) were isolated by positiveselection with anti-BDCA-2 microbeads (Miltenyi Biotec, Auburn, Calif.).Isolated pDC were added back into a pool of total PBMC to result infinal pDC concentrations in total PBMC varying from 0.5 to 2.4% bydonor.

Cells were resuspended in RPMI-1640 (BioWhittaker, Walkersville, Md.)supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gemini,West Sacramento, Calif.) plus 50 U/ml penicillin, 50 μg/ml streptomycin,2 mM L-glutamine, 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonicacid (HEPES) buffer and 1 mM sodium pyruvate (BioWhittaker,Walkersville, Md.). For B cell stimulation, cells were cultured at0.75×10⁶ per mL in 96-well round-bottomed plates in duplicate with PN orCC at a concentration range of 5.5-0.0054 μM for 90-93 h. For PBMC andpDC-enriched PBMC stimulation, cells were cultured at 2.5×10⁶ per mL in96-well flat-bottomed plates in triplicate with PN or CC at aconcentration range of 2.5-0.0012 μM for 21-24 h.

ELISA assays. IL-6 and IFN-α levels were assayed using commerciallyavailable antibody pairs (MabTech, Inc. Cincinnati, Ohio); the limit ofminimal detection was 31 pg/mL for IL-6 and 23 pg/mL for IFN-α. 96-wellMaxisorp Immuno plates were coated with cytokine specific Ab and thenblocked with 1% BSA in DPBS. Cell culture samples were added and boundcytokine was detected by addition of biotin-labeled secondary antibody,followed by horse radish peroxidase and a peroxidase-specificcolorimetric substrate. Standard curves were generated using recombinantcytokines purchased from R&D Systems (Minneapolis, Minn.) for IL-6 andMabTech for IFN-α. Absorbance values were determined at 450 nm withbackground subtraction at 650 nm using either a SpectraMax 190 orVersaMax microplate reader (Molecular Devices Corporation, Sunnyvale,Calif.). Half-maximal effective concentrations (EC₅₀) values werecalculated from each individual donor by interpolation with a cumulativeaverage for all donors tabulated. The EC₅₀ was defined as the PN or CCconcentration giving a value equal to half the maximum cytokine level.

Example B2 Isolation and Stimulation of Mouse Splenocytes

Activity of polynucleotides (PN) and chimeric compounds (CC) wereassessed in vitro by measurement of cytokine secretion by mousesplenocytes. Cytokine levels secreted into cell culture media weremeasured by enzyme-linked immunosorbent assay (ELISA).

Spleens of 8 to 20 week-old BALB/c mice were harvested and thesplenocytes isolated using standard teasing apart and treatment with ACKlysing buffer (BioWhittaker, Inc. Walkersville, Md.). Four spleens werepooled in the experiments. Cells were re-suspended in RPMI-1640supplemented with 10% heat-inactivated fetal bovine serum (FBS) plus 50μM 2-mercaptoethanol, 50 U/ml penicillin, 50 μg/ml streptomycin, 2 mML-glutamine, 10 mM HEPES and 1 mM sodium pyruvate. For stimulation,splenocytes were cultured at 3.5×10⁶ cells per mL in 96-wellflat-bottomed plates in triplicate with PN or CC at a concentrationrange of 22-0.0003 μM for 20-24 h.

ELISA assays. IL-6 and IL-12p40 levels were assayed using commerciallyavailable antibody pairs (BD Biosciences, San Jose, Calif.); the limitof minimal detection was 31 pg/mL for IL-6 and 63 pg/ml for IL-12p40.96-well Maxisorp Immuno plates were coated with cytokine specific Ab andthen blocked with 1% BSA in DPBS. Culture supernatants were added andbound cytokine was detected by addition of biotin-labeled secondaryantibody, followed by HRP and a peroxidase-specific colorimetricsubstrate. Standard curves were generated using recombinant cytokinespurchased from BD Biosciences. Absorbance values were determined at 450nm with background subtraction at 650 nm using either a SpectraMax 190or VersaMax microplate reader (Molecular Devices Corporation, Sunnyvale,Calif.). The EC₅₀ was defined as the concentration of PN or CC giving avalue equal to half the maximum cytokine level. EC₅₀ values for IL-6 andIL-12p40 were determined using a sigmoidal-dose response curve fit ofX=Log(X) transformed data using GraphPad Prism software.

Example B3 Linear Chimeric Compound (CC) Sequence Optimization

Two separate experiments were conducted. In the following tables themean refers to the geometric mean.

A. Experiment 1. Linear CC D56-14 was previously shown to induce IFN-αfrom human PBMC, IL-6 from human B cells and to stimulate mousesplenocytes (U.S. Pat. No. 8,597,665). Sequence optimization wasperformed to determine if the IFN-α activity could be improved relativeto D56-14. Seven new linear CC were tested in primary screening assays,i.e., human PBMC IFN-α activity, and human B cell IL-6 activity (seeExample B1 for procedures). The general structure of the linear CCs usedin this example, N₁-S₁-N₂-S₂-N₃, can be used to describe the placementof the nucleic acid motifs (N) within the CC. Six of the new CC in thisstudy all contained the mouse motif, 5-AACGTTC-3′, in the N₃ position.D56-24 contained the mouse motif in the N₂ position, and was included inthe screening to explore a different positioning of the mouse activitymotif in the linear CC context. D56-10 is a known CpG-Bimmunostimulatory sequence (ISS) and was included in the panel as apositive control.

TABLE B3-1 Experiment 1 CC Panel Human PBMC IFN-alpha Response EC50 (mM)Donor # D56-10 D56-14 C56-15 D56-16 D56-18 D56-19 D56-21 D56-22 D56-24Do 1 NC 0.061 0.057 0.045 0.047 0.104 ND ND ND Do 2 NC 0.102 0.109 0.0580.104 0.105 ND ND ND Do 3 NC 0.072 0.068 0.054 0.059 0.078 0.112 0.0670.029 Do 4 NC 0.071 0.094 0.065 0.085 0.095 0.142 0.070 0.051 Do 5 NC0.055 0.110 0.096 0.056 0.121 0.227 0.053 0.042 Do 6 NC 0.068 0.0790.059 0.077 0.145 0.187 0.056 0.050 Do 7 NC ND 0.129 0.096 ND 0.1250.377 0.122 0.081 Do 8 NC 0.056 0.112 0.059 0.100 0.109 0.333 0.0930.052 Ave NC 0.069 0.095 0.066 0.076 0.110 0.230 0.077 0.051 SD NC 0.0160.025 0.019 0.022 0.021 0.106 0.026 0.017 Count 0 7 8 8 7 8 6 6 6 SEM NC0.006 0.009 0.007 0.008 0.007 0.043 0.011 0.007 Mean NC 0.068 0.0920.064 0.073 0.109 0.210 0.074 0.048 NC = not calculable from doseresponse curve; ND = not determined for specified donors

TABLE B3-2 Experiment 1 CC Panel Human B Cell IL-6 Response EC50 (mM)Donor # D56-10 D56-14 C56-15 D56-16 D56-18 D56-19 D56-21 D56-22 D56-24Do 9 0.101 0.126 0.270 0.075 0.264 ND ND ND ND Do 10 0.097 0.053 0.1190.052 0.154 0.128 0.235 0.044 0.056 Do 11 NC 0.068 0.144 0.078 0.1590.146 0.341 0.066 ND Do 12 0.048 0.048 0.078 0.066 ND ND ND ND ND Do 13ND 0.056 ND 0.056 0.148 0.137 0.407 0.047 0.059 Do 14 0.052 0.053 0.0720.051 0.156 0.075 0.256 0.050 0.059 Do 15 0.120 0.081 0.183 0.056 0.2130.184 0.747 ND ND Do 16 0.084 0.128 0.217 0.116 0.219 ND ND ND ND Do 170.075 0.066 0.217 0.064 0.171 0.144 0.303 0.057 0.052 Ave 0.082 0.0750.162 0.068 0.185 0.136 0.382 0.053 0.057 SD 0.026 0.031 0.071 0.0200.042 0.035 0.189 0.009 0.003 Count 7    9    8    9    8    6    6   5    4    SEM 0.010 0.010 0.025 0.007 0.015 0.014 0.077 0.004 0.002 Mean0.079 0.071 0.147 0.066 0.182 0.131 0.352 0.052 0.056 NC = notcalculable from dose response curve; ND = not determined

Linear CC D56-16, D56-18, D56-19, and D56-22 and D56-24 showed similaror improved PBMC IFN-α activity (Table B3-1), and similar or slightlyreduced human B cell activity (Table B3-2) compared to D56-14. Linear CCD56-24 showed the best PBMC IFN-α and human B cell activity of sequencestested. As noted above, the principal difference between D56-24 and theother sequences is that N₂ and N₃ human and mouse motifs, respectively,are switched in D56-24 such that the mouse motif is located in the N₂position as compared to the N₃ position in the other new CC.

B. Experiment 2. Based on results from Experiment 1, a new panel of CCsequences was designed with the goal of increasing human and mouseactivity. Specifically, four new sequences related to D56-16, D56-18,D56-19, and D56-22 were designed with the mouse motif moved to the N₂position: D56-17, D56-01, D56-20, and D56-23. The initial in vitroscreening of the new CCs was performed on mouse splenocytes (Table B3-3and Table B3-4). All sequences with the mouse motif in the N₂ positionshowed strongly improved IL-6 and IL-12p40 potency compared to thecorresponding CCs with the mouse motif in the N₃ position. D56-01 andD56-23 showed the best IL-6 potency of the CCs tested while D56-01 hadthe best IL-12p40 potency.

TABLE B3-3 Experiment 2 CC Panel Mouse Splenocyte IL-6 Response EC50(mM) D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- Exp # 10 1424 16 17 18 01 19 20 22 23 426 0.046 0.071 0.031 1.293 0.032 2.359 0.0268.784 0.042 1.009 0.025 433 0.039 0.048 0.025 0.725 0.018 2.942 0.0175.942 0.026 1.422 0.012 Ave 0.042 0.060 0.028 1.009 0.025 2.651 0.0217.363 0.034 1.216 0.019 SD 0.005 0.016 0.004 0.402 0.010 0.412 0.0062.010 0.011 0.292 0.009 Count 2 2 2 2 2 2 2 2 2 2 2 SEM 0.004 0.0110.003 0.284 0.007 0.292 0.005 1.421 0.008 0.207 0.006 Mean 0.042 0.0590.028 0.968 0.024 2.634 0.021 7.225 0.033 1.198 0.017

TABLE B3-4 Experiment 2 CC Panel Mouse Splenocyte IL-12p40 Response EC50(mM) D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- Exp # 10 1424 16 17 18 01 19 20 22 23 426 0.078 0.821 0.341 1.369 0.339 1.225 0.2501.190 1.106 0.421 0.335 433 0.062 0.906 1.256 3.298 0.995 2.138 0.0914.507 2.901 3.229 2.410 Ave 0.070 0.864 0.798 2.334 0.667 1.682 0.1702.849 2.003 1.825 1.372 SD 0.011 0.060 0.647 1.364 0.464 0.645 0.1132.346 1.269 1.985 1.467 Count 2 2 2 2 2 2 2 2 2 2 2 SEM 0.008 0.0430.458 0.964 0.328 0.456 0.080 1.659 0.897 1.404 1.038 Mean 0.070 0.8620.654 2.125 0.581 1.619 0.151 2.316 1.791 1.166 0.898

Results for the human PBMC IFN-α activity and human B cell IL-6 activityare shown in Table B3-5 and Table B3-6, respectively. Surprisingly,having the mouse motif in N₂ position also significantly improved thehuman PBMC IFN-α potency. In general, the human IL-6 potency was alsoimproved for the CC with the mouse motif in the N₂ position.

Of the in vitro tests performed, IFN-α potency is considered the mostpredictive of good in vivo activity in cancer, antiviral, asthma, andallergy models. Based on this, D56-01, D56-17, D56-20, D56-23, andD56-24 were considered the lead candidates. These sequences also showedgood human B cell IL-6 and mouse IL-6 activity. Surprisingly, D56-01 hassignificantly improved IL12p40 potency compared to the other N₂ mousemotif sequences.

TABLE B3-5 Experiment 2 CC Panel Human PBMC IFN-α Response EC50 (mM)D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- Donor # 10 14 2416 17 18 01 19 20 22 23 Do 1 ND 0.044 0.029 0.031 0.049 0.055 0.0380.071 0.037 0.061 0.218 Do 2 ND 0.052 0.040 0.029 0.021 0.094 0.0390.091 0.029 0.053 0.024 Do 3 0.373 0.096 0.028 0.033 0.050 0.066 0.0480.117 0.101 0.054 ND Do 4 ND 0.059 0.048 0.045 0.045 0.064 0.036 0.0680.033 0.081 ND Do 5 ND 0.124 0.020 0.104 0.045 0.094 0.092 0.143 0.0610.106 ND Do 6 0.054 0.044 0.033 0.059 0.041 0.097 0.035 0.063 0.0380.067 0.048 Do 7 ND 0.055 0.036 0.054 0.027 0.067 0.028 0.099 0.0300.060 0.018 Do 8 ND 0.100 0.051 0.105 0.045 0.099 0.057 0.147 0.0690.122 ND Ave 0.213 0.072 0.036 0.058 0.040 0.080 0.047 0.100 0.050 0.0750.077 SD 0.226 0.030 0.010 0.031 0.011 0.018 0.020 0.033 0.025 0.0260.095 Count 2    8 8 8 8 8 8 8 8 8 4    SEM 0.160 0.011 0.004 0.0110.004 0.006 0.007 0.012 0.009 0.009 0.048 Mean 0.142 0.067 0.034 0.0510.039 0.078 0.044 0.095 0.045 0.072 0.046 ND = not determined

TABLE B3-6 Experiment 2 CC Panel Human B Cell IL-6 Response EC50 (mM)D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- D56- Donor 10 14 24 1617 18 01 19 20 22 23 Do 9 0.054 0.065 0.044 0.049 0.028 0.173 0.0530.090 0.048 0.041 0.024 Do 10 0.066 0.063 0.045 0.043 0.035 0.137 0.0210.096 0.017 0.045 0.018 Do 11 0.062 0.056 0.039 0.047 0.034 0.149 0.0500.128 0.041 0.045 0.027 Do 12 0.069 0.066 0.052 0.057 0.040 0.170 0.0520.122 0.033 0.048 0.029 Ave 0.063 0.063 0.045 0.049 0.034 0.157 0.0440.109 0.034 0.045 0.025 SD 0.006 0.005 0.005 0.006 0.005 0.017 0.0150.019 0.013 0.003 0.005 Count 4 4 4 4 4 4 4 4 4 4 4 SEM 0.003 0.0020.003 0.003 0.002 0.009 0.008 0.009 0.007 0.001 0.002 Mean 0.063 0.0630.045 0.048 0.034 0.157 0.041 0.108 0.032 0.045 0.024

Example B4 D56-05 Induces More Potent In Vitro Responses than D56-01

Based on potency of induction of both human and mouse cytokines, D56-01was chosen as a lead candidate to develop in a nanoparticle formulation.The D56-01 sequence was conjugated to FICOLL as described in Example S3to generate D56-05 (aka [(D56-01)-PEG₆]_(x)-FICOLL). D56-01 and D56-05were then compared for relative in vitro potency for induction of humanPBMC IFN-α and human B cell IL-6. Results for the human PBMC IFN-αactivity and human B cell IL-6 activity are shown in Table B4-1 andTable B4-2, respectively. The sequences D56-10 and D56-14 were used ashistorical positive controls in this experiment.

The nanoparticle formulation D56-05 was strikingly more potent ininduction of both IFN-α (Table B4-1) and IL-6 activity (Table B4-2).

TABLE B4-1 Human PBMC IFN-α Responses to D56-01 and D56-05 EC50 (mM)Donor # D56-10 D56-14 D56-01 D56-05 Do 1 NC NC NC 0.024 Do 2 0.109 0.0770.063 0.016 Do 3 0.319 NC 0.057 0.007 Do 4 0.198 0.070 0.050 ND Do 50.090 0.065 0.053 0.025 Do 6 0.187 0.081 0.033 0.005 Do 7 NC 0.091 0.0520.007 Do 8 0.122 0.052 0.045 0.007 Do 9 NC 0.053 0.054 0.007 Do 10 0.0820.068 0.057 0.019 Do 11 ND 0.050 0.042 NC Do 12 ND 0.058 0.038 0.027 Do13 ND 0.057 0.037 0.031 Do 14 ND 0.060 0.050 0.007 Do 15 ND 0.057 0.0530.010 Do 16 ND NC 0.026 0.003 Ave 0.158 0.064 0.047 0.014 SD 0.084 0.0130.010 0.010 Count 7    13    15    14    SEM 0.032 0.003 0.003 0.003GeoMean 0.142 0.063 0.046 0.011 NC = not calculable from dose responsecurve; ND = not determined

TABLE B4-2 Human B Cell IL-6 Responses to D56-01 and D56-05 EC50 (mM)Donor # D56-10 D56-14 D56-01 D56-05 Do 17 0.067 0.074 0.076 0.019 Do 180.078 0.072 0.065 0.015 Do 19 0.078 0.080 0.089 0.018 Do 20 0.061 0.0670.063 0.014 Do 21 ND 0.077 0.069 0.020 Do 22 ND 0.050 0.050 0.014 Do 23ND 0.051 0.054 0.011 Do 24 ND 0.073 0.073 0.018 Do 25 ND 0.057 0.0610.013 Ave 0.071 0.074 0.072 0.017 SD 0.008 0.005 0.010 0.003 Count 4   5    5    5    SEM 0.004 0.002 0.005 0.001 GeoMean 0.071 0.074 0.0720.017 ND = not determined

Example B5 D56-05 Induces More Potent In Vivo Responses than D56-01

Induction of innate immune responses following administration of D56-05and D56-01 to mice and cynomologus monkeys was evaluated. In monkeys,interferon-pathway associated gene expression was measured in bloodsamples collected prior to and 24 hours post administration of D56-05and D56-01. In mice, interferon-pathway and chemokine-associated geneexpression were measured in injection-site draining lymph nodesharvested 18 hours post compound administration. Relative ability ofantigen-presenting cell populations to acquire D56-05 and D56-01 wasevaluated in injection site-draining lymph nodes harvested from mice 24hours post compound injection. Additionally, maturation markerexpression (CD69, CD86) was measured on plasmacytoid dendritic cells(pDCs) from lymph nodes harvested 20 hours post compound injection.

Cynomolgus monkeys (Macaca fascicularis) were housed at ValleyBiosystems, (West Sacramento, Calif.) or at Battelle Biomedical ResearchCenter (Columbus, Ohio), where all in life procedures were carried out.Only healthy adult animals were used in each study. Whole blood wascollected in PAXgene tubes (QIAGEN, Venlo, NL) pre- andpost-immunization and frozen for later extraction of RNA according tothe manufacturer's instructions. Groups of 3 to 6 monkeys were immunizedby the intramuscular route (quadriceps) with 10 μg anthrax recombinantProtective Antigen (rPA) from PharmAthene (Annapolis, Md.) alone or incombination with 1000, 250 or 50 μg D56-05 or 1000 or 250 μg D56-01 in 1mL PBS.

For immunogenicity studies, groups of cynomolgus monkeys were immunizedby either the i.m. (quadriceps) or s.c. route with rPA with/withoutdoses of D56-01 or D56-05 in a total volume of 1 ml Dulbecco's PBS(DPBS) from BioWhittaker (Walkersville, Md.) with subsequent blood drawsto assess effects of adjuvants on Ab responses.

Swiss Webster, BALB/c, and C57BL/6 mice (8-12 weeks of age) werepurchased from Charles River Laboratoies (Hollister, Calif.) and housedat Pacific BioLabs (Hercules, Calif.) or Murigenics (Vallejo, Calif.),where all in life procedures were carried out. TLR9^(−/−) mice weremaintained at Simonsen Laboratories (Gilroy, Calif.) and used at 8-16 wkof age.

For immunogenicity, tissue distribution, and systemic toxicity studies,mice were injected in the quadriceps with adjuvant with/without rPA, orwith rPA alone. For studies assessing muscle tissue responses, mice wereinjected bilaterally in the quadriceps with adjuvant alone. For draininglymph node responses, including gene expression and flow cytometryassessments, mice were injected in both rear footpads with adjuvantwith/without rPA. D56-01-Alexa Fluor® 555, when used, was administeredin combination with nonlabeled D56-01 in a ratio to match Alexa Fluor®555/D56-05-specific relative fluorescence. All immunizations wereperformed in a total volume of 50 μL DPBS or 10 mM sodium phosphatebuffer.

For gene expression analysis, mice were injected by the intramuscular orsubcutaneous route (footpad) with DPBS or 10 μg D56-05 or D56-01. Muscletissue and draining lymph nodes were harvested at 6 hours or 18 hoursrespectively, into RNAlater (QIAGEN, Venlo, The Netherlends) and frozenfor later extraction of RNA according to the manufacturer'sinstructions. To quantify cellular uptake of compounds by flowcytometry, draining lymph nodes were harvested 24 hours after 25 μgfluorescently-labeled D56-01 or D56-05 was injected. Refer to ExamplesS2 and S15 for manufacture of Alexa Fluor® 555-(D56-01) and Alexa Fluor®555-(D56-05), respectively. For analysis of cell surface markers usingflow cytometry, draining lymph nodes were harvested 20 hours afterinjection of 5, 2, or 0.2 μg non-fluorescently-labeled D56-01 or D56-05.For flow cytometry experiments, single cell suspensions were preparedfrom treatment group pooled lymph nodes.

Organs were frozen in RNAlater (Qiagen, Venlo, The Netherlands). TotalRNA was isolated from 30 mg per individual homogenized muscle using anRNeasy fibrous tissue mini kit (Qiagen) and entire homogenized popliteallymph node using an RNeasy mini kit (Qiagen), both with on-column DNaseI digestion.

Reverse Transcription-Polymerase Chain Reaction (RT-PCR). cDNA wasprepared from total RNA samples using Recombinant RNasin RibonucleaseInhibitor (Promega, Madison, Wis.), Oligo(dT)15 (Promega), RandomPrimers (Promega), dNTP (Invitrogen, Carlsbad, Calif.) and SuperScriptIII Reverse Transcriptase (Invitrogen). Quantification of mRNA wasperformed using Power SYBR Green master mix (Life Technologies). Thecycling conditions were 15 min at 95° C., followed by 40 rounds of 15sec at 95° C. and 1 min at 60° C., with analysis by an AppliedBiosystems (Carlsbad, Calif.) StepOnePlus Real Time PCR system usingStepOne v2.1 software. Ubiquitin was used as the reference gene. AfterPCR, Ct values were determined and normalized data were expressed asfold increase over pre-immunization or DPBS control. Alternately, RNAwas reverse transcribed by an RT² First Strand Kit (Qiagen) for use withthe RT² Profiler PCR array system (Qiagen) for cytokines and chemokinesaccording to the manufacturer's directions.

Flow cytometry. Single-cell suspensions were prepared from mouse tissuesand pooled by experimental group, excepting muscle, which was firstdigested with 2 mg/ml collagenase, type 2 (Worthington BiochemicalLakewood, N.J.) for 45 min at 37° C. Cells were stained for 30 min at 4°C. in DPBS containing 0.1% BSA with/without 2 mM EDTA after blockingFcgR with clone 2.4G2 mAb. Cells were fixed in a final concentration of1% formaldehyde for a minimum of 20 min, followed by washing andresuspension in FACS flow buffer. Abs against CD3ε (145-2C11), CD4(GK1.5), CD8a (53-6.7), CD11b (M1/70), CD11c (HL3), CD19 (6D5),CD45R/B220 (RA3-6B2), CD49b (DX5), CD69 (H1.2F3), CD86 (GL-1), CD95(Jo2), CD279 (J43), CD317/PDCA-1 (eBio927), CXCR5 (2G8), F4/80 (BM8),Ly-6C (AL-21), Ly-6G (1A8), MHC class II (MHC II; I-A/I-E)(M5/114.15.2), and T and B Cell activation Ag (GL7) were purchased fromBD Biosciences (San Jose, Calif.), BioLegend (San Diego, Calif.), oreBioscience (San Diego, Calif.). Biotinylated peanut agglutinin (PNA)was purchased from Vector Laboratories (Burlingame, Calif.). Flowcytometry data were collected on an LSR II (BD Biosciences, San Jose,Calif.) flow cytometer and analyzed using FlowJo software (Tree Star,Ashland, Oreg.). Polychromatic imaging flow cytometry data werecollected on an ImageStreamX mk II (Amnis, Seattle, Wash.) and analyzedusing IDEAS v6.1 software. Images were captured using a 360 lens with a0.9 numerical aperture and 2.5-mm effective depth of field. Cells likelyto have colocalized fluorescent signals were identified with aid ofbright detail similarity (BDS). BDS scoring quantifies colocalizationbetween fluorescent markers within cells by comparing the spatiallocation and degree of overlap to calculate the non-mean-normalizedPearson correlation coefficient of the images. Events with BDS scoresover the threshold level of 2 were likely to have fluorescencecolocalization, which was confirmed visually. Lymph node cells werestained with antibodies to identify pDCs (CD3⁻, CD19⁻, CD49b⁻, MHCII⁺,CD11c⁺, and B220⁺or PDCA-1⁺), cDCs (MHCII⁺, CD11b⁻, CD11c⁺), and mDCs(MHCII⁺, CD11b⁺, CD11c⁺) and markers of cell maturation (CD69 and CD86).Primary gating was through light scatter, doublet exclusion andlymphocyte lineage exclusion gating. Extent of fluorescently-labeledD56-05 and D56-01 uptake on pDCs, cDCs, and mDCs and, in a separateexperiment, maturation marker expression on pDCs (geometric meanfluorescence intensity; gMFI) was determined using FlowJo software(TreeStar, Ashland, Oreg.).

Statistical analysis. A Mann-Whitney or Kruskal-Wallis test with a Dunnposttest, as specified in the brief description of the drawings, wasused to determine statistical significance. A p value less than or equalto 0.05 was considered significant.

Results. Table B5-1 shows IFN pathway-associated gene expression inmonkey blood (fold increase over pre-immunization). These data indicatethat while D56-01 induced IFN-associated gene expression, D56-05 inducedmore intensive IFN-associated gene expression following immunizationwith rPA in primates.

To assess early D56-05 effects in local tissue that may be associatedwith improved adjuvant activity compared with monomeric D56-01,transcriptional changes were analyzed in injection site muscle 6 hoursafter injection. Mice were injected with adjuvants, without rPA, atequivalent CpG-based doses, with PBS-injected animals serving ascontrols. D56-05 exhibited a more potent effect on both the number ofgenes induced and the level of gene induction compared with the effectof monomeric D56-01, both for multiple IFN-regulated genes (IRGs) (FIG.11A) and chemokines (FIG. 11B). Likewise, D56-05 induced higher levelsof cytokines of the IL-1 and TNF superfamilies (FIG. 11C). Adhesionmolecules, integrins, and matrix metalloproteinases were also induced toa much greater degree in injection site muscle following D56-05treatment (FIG. 11D). Thus, D56-01 in a nanoparticle-like formulation ismore efficient at inducing early markers of immune activation at theinjection site compared with monomeric D56-01. To determine whethernanoparticulate and monomeric D56-01 differentially affected cellularrecruitment to injection site muscle, relative proportions of immunecell populations were analyzed by flow cytometry. At 24 h, total CD45+cells were 3-fold as abundant in D56-05-injected muscle compared withD56-01-injected tissue (about 212,000 versus about 67,000 cells/gmuscle). D56-05 injection induced relatively higher proportions ofconventional DCs (cDCs), myeloid DCs (mDCs), myeloid cells, macrophages,monocytes, and neutrophils in the injected muscle compared with miceadministered monomeric D56-01 (FIG. 11E).

To test whether D56-05-induced inflammatory gene expression andadjuvanticity for rPA-induced Ab responses involved TLR9-independentpathways, responses were tested in TLR9^(−/−) mice. Following i.m.injection with D56-05, induction of IRGs and chemokine and cytokinegenes was observed in wildtype C57BL/6 mice, but not in TLR9^(−/−) mice(FIG. 12A). Consequently, no D56-05 adjuvant activity was observed inTLR9^(−/−) mice (FIG. 12B). The lack of both inflammatory responsesinduced at the injection site and adjuvant effects in TLR9^(−/−) micedemonstrated that the activity of D56-05 is dependent on TLR9 signaling.

18 hours after s.c. injection, D56-05 produced greater increases intranscription of interferon-regulated genes (FIG. 13A), chemokines (FIG.13B), and cytokines (FIG. 13C) in lymph nodes compared with D56-05. As alikely consequence of stronger induction of multiple chemokines, D56-05injection resulted in greater numbers of various antigen presenting cell(APC) populations in the draining lymph node compared withD56-01-injected mice. MHC II+ pDCs were especially affected, with 5-foldgreater numbers present (mean, 940 versus 187 cells/lymph node)following D56-05 treatment (FIG. 14). Taken together, these datademonstrate that D56-05 is more potent than monomeric D56-01 forinitiating immune responses at the injection site and in draining lymphnodes.

Whether relative increases in cellular trafficking following D56-05treatment were accompanied by differential effects on cellular uptake ofthe adjuvant were determined. A wide range of cell populations involvedin the initiation of adaptive immune response, including MHC II+ pDCsand mDCs, myeloid cells, macrophages, and monocytes, as well asneutrophils, all demonstrated greater fluorescence following injectionwith D56-05. There were substantial proportions of mDCs, myeloid cells,macrophages, and monocytes with high levels of Alexa Fluor® 555fluorescence in D56-05-injected mice, whereas only mDCs internalizedD56-01 to a similar extent. Lymphocyte uptake of either Alexa Fluor®555-labeled D56-01-Ficoll or D56-01 was negligible. Table B5-2 showsuptake of fluorescently-labeled D56-05 or D56-01 as measured bygeometric Mean Fluorescence Intensity (gMFI) of A555-labeled D56-05 orD56-01 in cells. These data indicate that draining lymph node pDC, cDCs,and mDCs take up D56-05 or D56-01 following in vivo injection in mice.In general, uptake of D56-05 was greater than uptake of D56-01 in thedifferent cell populations as indicated by higher gMFI values.

D56-05 also exerted a greater effect on the activation state of APCs andlymphocytes than did monomeric D56-01 within the draining lymph nodes.Following D56-05 injection, pDCs, CD8+ DCs, cDCs, mDCs, and myeloidcells all displayed greater expression of CD86, whereas B and NK cellsdisplayed greater expression of CD69 compared with lymph node cellsharvested from mice injected with monomeric D56-01. Table B5-3 displayslevels of CD69 and CD86 expression on pDCs from mouse lymph nodes. Thesedata indicate that both D56-05 and D56-01 induce CD69 and CD86expression on pDCs but D56-05 is more potent in inducing maturation ofpDCs in vivo as compared to D56-01. Thus, nanoparticulate formulation ofD56-01 on Ficoll substantially improves its uptake by and activation ofkey APC populations, contributing to the effective induction of adaptiveimmunity.

To determine whether Ficoll conjugation increased the efficiency ofCpG-ODN and Ag uptake into the same cells, mice received footpadinjections with fluorescently labeled adjuvants (as described above)plus rPA labeled with Alexa Fluor® 647. Popliteal lymph node cells wereharvested 24 or 48 hours after injection for flow cytometry analysis.For each APC type examined, many cells incorporated only Ag or adjuvant;however, there was also a population of cells that acquired both rPA andD56-05 or D56-01. Mice immunized with D56-05 and rPA demonstrated thehighest frequency of APCs with coincident Ag and adjuvant uptake as wellas cells with adjuvant uptake only. Polychromatic imaging flow cytometryand subsequent calculation of BDS scoring in two additional experimentswere employed to determine whether Alexa Fluor® 555-labeled D56-05 andAlexa Fluor® 647-labeled rPA specifically colocalized within the samecells. Approximately 11% of pDCs, 7% of mDCs, 5% of myeloid cells, and<1% of cDCs with joint D56-05 and rPA uptake demonstrated BDS scoresgreater than 2, indicating likely colocalization of Ag and adjuvantwithin cells at the time of measurement.

The impact of D56-05 on GC B and T follicular helper (T_(FH)) cellresponses within the injection site draining lymph nodes were evaluated.This was directly evaluated by flow cytometry, identifying GC B cells asB220+/GL7+/PNA+/CD95+ cells and T_(FH) cells as CD4+/CXCR5+/PD1+ cells.Mice were immunized once in the footpad with rPA with/without D56-05 orD56-01 or vehicle control, with numbers of GC B or T_(FH) cellsmonitored for 2 wk. Higher proportions of GC B and T_(FH) cells weredetected in draining lymph nodes of rPA/D56-05 immunized mice by day 5and remained elevated at day 14. GC B and T_(FH) responses were minimalin rPA only immunized mice compared with vehicle-injected mice. Takentogether, these data suggest that the increased potency of D56-05 overD56-01 for induction of innate immunity is reflected in early GC B and Tcell responses.

TABLE B5-1 Fold Induction of IFN Pathway-associated Genes OverPre-immunization in Blood of Individual Monkeys in Response toImmunization with rPA ± D56-05 or D56-01 GBP- IFN- IL- IRF- ISG-Immunizations 1 α 6 7 54 Mxb p28 rPA (10 μg) 1.0 2.0 2.9 0.6 1.4 1.1 2.6rPA (10 μg) 0.4 0.7 0.4 0.3 0.5 0.7 0.3 rPA (10 μg) 0.9 1.6 0.5 0.5 0.81.0 0.6 1000 μg D56-01 + rPA 2.0 0.9 0.7 0.7 9.6 4.6 0.7 1000 μgD56-01 + rPA 2.1 0.2 1.1 1.4 19.7 6.1 1.5 1000 μg D56-01 + rPA 2.8 0.20.9 0.6 7.2 5.0 0.8 1000 μg D56-01 + rPA 1.2 0.5 0.3 0.8 7.3 5.9 0.21000 μg D56-01 + rPA 2.1 0.1 0.4 0.6 5.6 7.1 0.2 250 μg D56-01 + rPA 0.62.9 1.1 0.5 1.3 1.2 0.4 250 μg D56-01 + rPA 0.4 0.4 0.5 0.2 0.5 0.7 0.4250 μg D56-01 + rPA 2.6 0.2 1.0 0.9 14.2 9.5 0.4 250 μg D56-01 + rPA 0.71.2 0.8 0.9 2.8 2.4 0.8 250 μg D56-01 + rPA 0.9 0.8 1.0 0.8 2.5 1.8 0.9250 μg D56-01 + rPA 1.6 0.9 0.6 0.9 4.4 3.2 0.9 1000 μg D56-05 + rPA 3.60.5 2.2 1.5 16.4 7.9 1.1 1000u μ D56-05 + rPA 20.3 0.8 1.7 4.1 74.3 26.61.9 1000 μg D56-05 + rPA 10.3 1.3 0.9 2.4 30.8 14.3 0.8 1000 μg D56-05 +rPA 29.5 0.3 2.3 3.1 69.7 35.9 2.7 1000 μg D56-05 + rPA 2.1 0.4 0.9 0.88.2 5.2 0.8 250 μg D56-05 + rPA 14.7 3.6 2.7 4.3 61.8 19.9 1.3 250 μgD56-05 + rPA 11.6 0.8 1.1 1.9 44.2 17.4 2.1 250 μg D56-05 + rPA 2.6 0.32.0 1.2 10.5 5.1 0.9 250 μg D56-05 + rPA 11.3 1.0 1.4 3.1 56.9 19.2 1.7250 μg D56-05 + rPA 9.5 1.1 2.8 4.5 45.2 18.9 4.0 250 μg D56-05 + rPA0.9 0.2 1.0 0.6 1.1 1.8 0.4 50 μg D56-05 + rPA 7.0 0.7 2.5 2.6 20.3 10.12.5 50 μg D56-05 + rPA 5.2 0.2 0.5 0.9 9.9 7.1 0.6 50 μg D56-05 + rPA0.9 0.4 0.6 0.7 4.9 4.5 1.0 50 μg D56-05 + rPA 2.9 1.0 1.8 1.9 5.7 4.01.5 50 μg D56-05 + rPA 6.0 1.0 2.8 5.5 41.4 14.3 4.5 50 μg D56-05 + rPA4.7 1.2 0.4 1.1 9.2 8.2 0.8

TABLE B5-2 Uptake of Fluorescently Labeled Compounds (Geometric MeanFluorescence Intensity) in Draining Lymph Node Cells from MiceAdministered D56-05 or D56-01 Exp No. D56-05 uptake (gMFI) D56-01 uptake(gMFI) pDC (MHCII⁺CD11b⁻CD11c⁺(B220⁺ or PDCA1⁺) Cells 1 165  50 2 379324 cDC (MHCII⁺CD11b⁻CD11c⁺) Cells 1  84  57 2 267 198 mDC(MHCII⁺CD11b⁺CD11c⁺) Cells 1 156 162 2 596 544

TABLE B5-3 Geometric Mean Fluorescence Intensity of CD69 and CD86Expression on Draining Lymph Node pDCs from Mice Administered D56-05 orD56-01 D56-05 D56-01 Exp No. DPBS 5 μg 2 μg 0.2 μg 5 μg 2 μg 0.2 μg CD69Expression (gMFI) 1 369 4378 2494 553 1703 1409 710 2 20 1193 1408 160431 287 161 CD86 Expression (gMFI) 1 412 1299 1243 541 556 529 458 2 3881536 958 562 717 910 579 3 70 711 519 105 105 105 90

Example B6 D56-05 Adjuvants Rapid, High Titer Toxin NeutralizingAntibody Responses to rPA and Protects Monkeys Against Lethal Challengewith Live Bacillus Anthrax Spores

The ability of D56-05 to induce protective antigen-specific antibodyresponses in a mammalian subject (i.e., immunogenicity) was evaluated inmonkeys immunized with D56-05+rPA. For comparison, additional groups ofmonkeys were immunized with D56-01+rPA or rPA alone. To test protectionfollowing one or two immunizations with D56-05, monkeys were challengedwith a lethal dose of anthrax spores and monitored for survival.

In life procedures for the monkey immunogenicity study are describedunder Example B5. For the anthrax aerosol challenge study, monkeys(Macaca fascicularis) were housed at Battelle Biomedical Research Center(Columbus, Ohio) where all in life procedures were carried out. 25 maleand 25 female healthy monkeys, previously not exposed to anthrax, wererandomized by weight into groups of eight (4 male, 4 female) or six (3male, 3 female). Animals were immunized by the i.m. route in thequadriceps on days 0 and/or 29 with 10 μg rPA in combination with either1000 or 250 μg D56-05 in a total volume of 1 mL DPBS. A group comprisedof six non-immunized animals was also included. Serum samples werecollected during the study to confirm development of antibody responses.Monkeys were exposed to a target dose of 200×50% lethal dose (LD₅₀)equivalents of aerosolized B. anthracis Ames spores on day 69, 70 or 71.Monkeys were randomized to one of the three challenge days, with atleast two monkeys from each group assigned to each day. The animals weremonitored twice daily for survival and clinical signs of illness for 28days following challenge. Any animal judged to be moribund wasimmediately euthanized. Qualitative bacteremia was assessed from day 62onward by streaking 30-40 ml EDTA whole blood onto blood agar plates andincubating at 37° C. for at least 48 h. Samples resulting in anycolonies consistent with B. anthracis morphology (g-hemolytic, whitecolonies, 4-10 mm in diameter with a rough appearance and irregularedges) were documented as positive.

Toxin Neutralization Assay (TNA). Development of antibody titers to rPAwas assessed by the in vitro Toxin Neutralization Assay (TNA). The assaymeasures the ability of serum antibodies to rPA to specifically protectJ774.1 cells against Bacillus anthracis lethal toxin cytotoxicity.J774.1 murine macrophages (American Type Culture Collection, Manassas,Va.) were exposed to PA and Lethal Factor (LF; List BiologicalLaboratories, Campbell, Calif.) in the presence or absence of seriallydiluted serum samples. Viability was assessed by addition of MTT(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). Titerswere calculated as the reciprocal of the dilution of a serum sample thatresults in 50% neutralization of toxin-mediated cytotoxicity (ED₅₀),corresponding to the inflection point of a 4-parameter logistic log fitof the neutralization curve. TNA results are reported as the quotient ofthe ED₅₀ of the test sample and the ED₅₀ of a reference standard (NF₅₀).Assay end points were calculated using SoftMaxPro version 4.7.1(Molecular Devices, Sunnyvale, Calif.). TNA assays were performed byDynavax Technologies except on sera arising from days −1, +1, +3, +5,+7, +14, +21 and +28 relative to challenge which were performed atBattelle, with NF₅₀ values calculated using human reference standardAVR801. Assay end points were calculated using SAS (JMP, Cary, N.C.).Data acquisition and analysis were performed by a SpectraMax 190 orVersa-Max using SoftMaxPro version 5.0.1 (Molecular Devices, Sunnyvale,Calif.) or SAS (SAS Institute, Cary, N.C.). The lower limit ofquantitation (LLOQ) was 100. Samples resulting in undetectable valueswere assigned a value equal to half the LLOQ.

Anti-rPA IgG quantification. Plates (96 well) were coated with rPA andincubated overnight. Standards and test sera, at appropriate dilutionseries, were assayed in duplicate. HRP-conjugated goat anti-human IgG(SouthernBiotech, Birmingham, Ala.) was used for detection and color wasdeveloped with a 3,3′,5,5′-tetramethylbenzidine Microwell PeroxidaseSubstrate System (KPL, Gaithersburg, Md.). Titers were calculated as thereciprocal of the dilution (ED50), corresponding to the inflection pointof a four-parameter logistic log fit curve. Results are reported as thequotient of the ED50 of the test sample and the ED50 of a referencestandard (NF50). Data acquisition and analysis were performed by aSpectraMax 190 or VersaMax using SoftMaxPro v5.0.1 software (MolecularDevices).

Results. Table B6-1 and FIG. 15A show immunogenicity study data,specifically TNA titers induced in monkey serum 2 weeks following asingle injection of rPA alone, rPA+D56-05, or rPA+D56-01 (individualtiters, geometric mean and 95% confidence interval). The two highestdoses of D56-05 induced mean TNA titers that were significantly higherthan in animals given only rPA, compared with a nonsignificant increaseby D56-01 addition. At the highest dose of D56-05, the calculated31-fold increase in TNA titers compared with rPA alone is likely anunderestimate of the adjuvant potency, as titers in rPA only animalswere all below the level of detection for the TNA assay. Additionally,all animals (11 of 11) receiving 250-1000 mg D56-05 were seropositivewhereas 5 of 11 animals immunized with 250-1000 mg D56-01 were below theLLOQ. These data indicate that both rPA+D56-05 and rPA+D56-01 inducedrapid and potent titers of toxin neutralizing antibodies compared toimmunization with rPA alone, but that TNA titers were highest in monkeysimmunized with equivalent CC amounts of D56-05.

Likewise, titers of total anti-rPA IgG at 14 days were significantlyincreased following immunization with rPA/D56-05 (FIG. 15B) and weresignificantly correlated to the TNA results (FIG. 15C). Following thesecond immunization at day 28, a >15-fold boost in TNA responses wasevident in all groups and the titers remained elevated for at least 18wk. The memory response to antigenic challenge about 5 mo following asecond immunization was also evaluated in these animals. Furtherincreases in TNA titers of at least 15-fold (FIG. 15D) demonstrated arapid, robust response, indicating potentially protective immunity.

To directly evaluate protection, cynomolgus macaques were immunized i.m.with rPA plus D56-05 once (day 29) or twice (days 0 and 29) andchallenged with a targeted dose of 200 LD50 equivalents of aerosolizedB. anthracis spores on day 70±1. Survival, bacteremia, and symptoms ofclinical disease were monitored for 28 days following challenge andserum samples collected before and after challenge for determination ofTNA titers. FIG. 16A shows Kaplan-Meier survival analysis for monkeyschallenged with aerosolized live anthrax spores following one or twoimmunizations with rPA+D56-05. Complete protection from anthraxchallenge was achieved in all monkeys receiving a single vaccination ofrPA with 1000 mg D56-05 or two vaccinations with either 250 or 1000 mgD56-05, whereas all unvaccinated animals succumbed to disease within 9days of challenge. These data clearly indicate that a singleimmunization with rPA+D56-05 protects 100% of monkeys from lethalchallenge. Animals immunized twice were also protected.

Furthermore, no animals vaccinated with rPA/D56-05 showed bacteremia orclinical symptoms at any time point after challenge. Followingchallenge, all animals produced a rapid increase in TNA titers,indicating a strong memory response. The memory response was striking inmonkeys receiving a single rPA/D56-05 immunization, rising rapidly tolevels comparable to twice-immunized animals within 7 days of theinfectious challenge (FIG. 16B). Taken together, these data demonstratethat a single immunization of rPA plus 1000 mg D56-05 primes animals fora prominent recall response and provides protection against lethalchallenge with aerosolized B. anthracis spores.

Although rapid, single-injection protection against anthrax exposurerepresents an unmet need, the potent adjuvant activity of D56-05suggested that substantially reduced doses may be effective insituations where a two-injection prophylactic regimen is feasible.Therefore, in a separate experiment, TNA responses were monitored inmonkeys immunized on days 0 and 28 with rPA and D56-05 at 1000, 50, 20,or 5 mg. TNA titers greater than 1000 were elicited in thetwo-immunization regimen, even with a D56-05 dose of 5 mg, the lowestdose tested, and were further boosted to greater than 10,000 by Ag onlyinjection (used as a surrogate for bacterial spore exposure) (FIG. 16C).Thus, in the context of a two immunization regimen, the data suggestprotective capacity with 1/200 of the D56-05 dose demonstrated to beprotective in a single-immunization regimen in monkeys.

Improved adjuvant activity by the D56-05 nanoparticle formulation wasalso evaluated in mice. Indeed, rPA/D56-05 induced significantly higherTNA titers after both a first and second immunization in mice,demonstrating the relevance of the species for studies investigating theD56-05 mechanism of action (FIGS. 17A-B).

TABLE B6-1 TNA Titers in Monkey Serum 2 Weeks Post First Immunizationwith rPA + D56-05, rPA + D56-01, or rPA rPA rPA/D56-05 rPA/D56-05rPA/D56-05 rPA/D56-01 rPA/D56-01 (10 μg) (1000 μg) (250 μg) (50 μg)(1000 μg) (250 μg) 50 5021 1270 1431 50 50 50 4163 1089 618 50 50 50 772137 168 223 365 2223 881 1304 256 50 1067 546 872 934 435 3081 50 192GeoMean 50 2073 809 451 168 125 95% CI (50-50) (5739-749) (2407-272)(1817-112) (782-36) (372-42)

Example B7 At Equivalent Doses, the Nanoparticle Formulation D56-05Demonstrates a Safety Advantage in Mice Compared to Free Linear ChimericCompound D56-01

To test the effect of nanoparticle formulation on thesafety/tolerability of CC sequences in vivo, mice were administeredrepeated high dose injections of D56-05 and D56-01 by the intramuscularroute. As a species in which to assess toxicity, mice demonstrate anexaggerated pharmacological response to CpG ODN-containing nucleotides,compared to primates, due to more widespread cellular distribution ofTLR9 expression in the mouse. We measured serum cytokine responses andmonitored changes in body weight in mice receiving 100 μg (based onD56-01 weight) of either D56-05 or D56-01 every 2 weeks for a total of 4injections in order to assess relative safety of the free andnanoparticle versions of the CC.

Female BALB/c mice (6-10 weeks of age) were purchased from Charles Riverand housed at Murigenics (Vallejo, Calif.) where all in life procedureswere carried out. Groups of 5 mice were administered 100 μg D56-05 orD56-01 once, twice, three, or four times with 2 weeks betweeninjections. Select groups were sacrificed 2 hours after each injection.For controls, one group received no injections and another group wasadministered injection vehicle (Saline, 50 μL). Both these groups weresacrificed 18 hours after the fourth injection. Serum was harvested bycardiac puncture at time of sacrifice. Spleen, liver and kidneys wereharvested at sacrifice and weighed. Mice were weighed twice weeklythroughout the study.

ELISA. Cytokine levels in serum samples were measured using commerciallyavailable antibody pairs as described under Example B1. Antibody pairsfor detection of mouse IL-6 and IL-12p40 were sourced from BDBiosciences (San Jose, Calif.). Reagents for detection of mouse IP-10,MCP-1, and TNF-α were sourced from R&D Systems (Minneapolis, Minn.). Thelimits of detection for these assays ranged from about 20 pg/mL to about150 pg/mL. Data acquisition and analysis were performed by a SpectraMax190 or VersaMax using SoftMaxPro v5.0.1 software (Molecular Devices).

D56-05 or D56-01 tissue quantification by enzyme-linked hybridizationassay or hybridization assay. Spleen, liver, kidney, or injection sitemuscle, 25-50 mg per tissue per individual animal, and draining lymphnodes, pooled per individual animal, were homogenized in 20 mM Tris (pH8), 20 mM EDTA (Sigma-Aldrich, St. Louis, Mo.), 100 mM sodium chloride,0.2% SDS (Teknova, Hollister, Calif.) using the TissueLyser II (Qiagen),and subject to proteinase K (New England BioLabs, Ipswitch, Mass.)digestion at 1.2 U/mg tissue for 6-20 hours at 50° C. Nunc Immobilizeramino plates were coated overnight at 4° C. with 30 ng/ml capture probe(5′-GCGCCGAGAA CGTTGCGCCG A-3′ set forth as SEQ ID NO:18 for D56-01quantification; and 5′-AGCCGCGTTG CAAGAGAAGC GATGCGCGGC TCG-3′ set forthas SEQ ID NO:19 for D56-05 quantification) in 0.1 M sodium phosphate(Teknova). For quantification of D56-05, homogenized samples, mixed inequal volume with 0.6 mg/ml detection probe (5′-GCGCCGAGAA CGTTGCGCCGA-3′ set forth as SEQ ID NO:18), were incubated for 75 min at 52° C. Forquantification of D56-01, homogenized samples, mixed in equal volumewith SSC plus 2% N-lauroylsarcosine sodium salt buffer, were incubatedfor 2 hours at 45° C. and allowed to cool for 30 min at roomtemperature. Synthesis of complementary 39 ends of captured D56-01 wascatalyzed by 1.25 U Klenow fragment (New England BioLabs) in thepresence of 0.5 mM biotinylated dUTP and 50 mM dNTP (New EnglandBioLabs). HRP-conjugated streptavidin (Thermo Scientific, Waltham,Mass.) was used for adjuvant detection, and color was developed with a3,3′,5,5′-tetramethylbenzidine microwell peroxidase substrate system(KPL). Adjuvants served as standards. The LLOQs were 6.24 and 7.62 ng/gtissue for D56-05 and D56-01, respectively. All data acquisition andanalysis were performed by a SpectraMax 190 or VersaMax using SoftMaxProv5.0.1 software (Molecular Devices).

Results. To test whether D56-05 and monomeric D56-01 displayeddifferential tissue distribution kinetics following i.m. injection, micewere injected with D56-05 or D56-01 and levels of the adjuvants at theinjection site and draining lymph nodes as well as at distal sites(spleen, liver, and kidney) were measured. Mice received a high dose(100 μg) of either adjuvant to facilitate recovery, and tissues wereharvested 1 day after injection. D56-05 and D56-01 were quantified byhybridization assays as described above. D56-05 was concentrated ininjection site muscle and lymph nodes (popliteal, inguinal, sciatic,lumbar, and sacral), whereas D56-01 quickly distributed systemically(FIG. 18). D56-01 was detected at minimal levels at the injection siteand lymph nodes, and instead concentrated in the spleen, liver, andkidney. These data indicate that nanoparticle and monomeric D56-01differentially distribute within 24 hours of injection, suggesting thatpreferential local retention of D56-05 may contribute to its increasedpotency as an adjuvant.

All of the systemic toxicities commonly observed in mice followingCpG-ODN administration were greatly reduced in animals injected withD56-05 compared with D56-01. Table B7-1 shows serum cytokine levels inmice 2 hours after administration of the first dose of either D56-05 orD56-01. The inflammatory cytokines IL-6, IL-12p40, IP-10, MCP-1 andTNF-α were all induced at high levels in the blood 2 hours after D56-01injection but not in response to D56-05.

Additionally, there was little evidence of a delayed systemic effect inD56-05-injected mice. Mice sacrificed after four biweekly injections ofD56-05 demonstrated spleen and liver weights similar to sham-injectedmice. Mice administered D56-01, but not D56-05, developed splenomegalyand hepatomegaly evident after 2 injections, which became morepronounced after 3 and 4 injections. This data is summarized in TableB7-2. There was no effect on kidney weight. Histopathological changes inD56-05-injected mice were minimal, whereas repeated D56-01 injectionsresulted in increased splenic extramedullary hematopoietic activity andhepatic changes, including cellular infiltration of sinusoids,hepatocellular alterations, and mild/moderate liver necrosis.

FIG. 19 shows group-averaged body weights over the study for micereceiving D56-05 and D56-01. Marked body weight loss, aTNF-alpha-dependent, CpG-induced toxicological event specific torodents, occurred in animals administered biweekly D56-01 injections. Incontrast, body weights were only slightly lower than those of controlsfor mice administered biweekly injections of high-dose D56-05. This datahas been adjusted to remove the effect the additional weight due tosplenomegaly and hepatomegaly in mice administered D56-01 anddemonstrates that overall body weight decreases with successiveadministrations of high dose D56-01 but not D56-05. Together, these datashow a marked safety advantage of nanoparticle-formulated D56-05 overfree CC D56-01. Unlike the free CC, the nanoparticle formulation doesnot induce inflammatory serum cytokine responses, appreciableorganomegaly or dramatic reduction in body weight, even after repeatedhigh-dose injections. Thus, the improved adjuvant activity of D56-05nanoparticles over monomeric D56-01 is accompanied by reduced systemictoxicity signals.

TABLE B7-1 Serum Cytokine Levels in Mice 2 h After a Single Dose of 100μg D56-05 or D56-01 Cytokine D56-05 D56-01 (pg/mL) Mean SEM Mean SEMIL-6 20 0 491 62 IL-12p40 1043 129 33273 3671 IP-10 78 0 1179 160 MCP-133 4 3871 327 TNF-α 33 6 965 91

TABLE B7-2 Organ Tissue Weights in Mice Administered 1-4 Doses of 100 μgD56-05 or D56-01 # of Liver in grams (Mean ± SEM) Spleen in grams (Mean± SEM) Injections D56-05 D56-01 Saline None D56-05 D56-01 Saline None 10.8 ± 0.03 0.9 ± 0.02 — — 0.1 ± 0.01 0.1 ± 0.01 — — 2 1.0 ± 0.04 1.8 ±0.1  — — 0.2 ± 0.01 0.5 ± 0.03 — — 3 0.9 ± 0.03 2.8 ± 0.2  — — 0.2 ±0.01 0.8 ± 0.06 — — 4 1.0 ± 0.03 3.2 ± 0.08 0.8 ± 0.03 0.8 ± 0.02 0.3 ±0.02 1.0 ± 0.07 0.07 ± 0.01 0.08 ± 0.01

Example B8 Intra-Tumoral Administration of D56-05 Suppresses TumorGrowth in Mice with Lymphoma Cell Line EG7-OVA Tumors

To test the application of D56-05 in a model of cancer immunotherapy(Moore et al., Cell, 54:777, 1998), the lymphoma cell line EG7 1 OVA wasused to assess the effect of intratumoral injection of D56-05 or acontrol non-CpG-containing oligonucleotide (D56-30) on growth ofestablished tumors.

Female C57BL/6 mice (6-10 weeks of age) were purchased from Harlan andhoused at Murigenics (Vallejo, Calif.) where all in life procedures werecarried out. 1×10*6 EG-7 cells (American Type Culture Collection,Manassas, Va.) were injected subcutaneously into the flank of C57BL/6mice. Starting on study day 0 (4 days after cell implantation) mice(N=5/group) were administered injections into the established tumor massof 50 μg D56-05 or a control non-CpG oligonucleotide (D56-30) in avolume of 150 μL of PBS. Injections were administered daily on Days 0,3, and 7. Animals were observed and tumor size (volume) was measured.

Tumor volume data is shown in FIG. 20. The data demonstrate that D56-05administered by the intratumoral route inhibited tumor volume increasein this murine tumor model.

Example B9 In Vitro Potency Evaluation of D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) Conjugates with Different D56-01:FICOLLMolar Ratios (x)

The effect of varying the D56-01:FICOLL molar ratio (x) in D56-05 (aka[(D56-01)-PEG₆]_(x)-FICOLL) conjugates on the potency of the biologicalresponse was assessed by means of an in vitro analysis. The in vitropotency in human B cells was determined as described in Example B1 forD56-05 conjugates with different D56-01:FICOLL molar ratios (x): D56-05x=24, D56-05 x=53, D56-05 x=82, D56-05 x=124 and D56-05 x=154. Resultsfor the human B cell IL-6 assay are shown in Table B9-1. Refer toExample S12 for the synthesis of D56-05 with different D56-01:FICOLLmolar ratios (x).

These data indicate that D56-05 conjugates with higher D56-01: FICOLLmolar ratios (x) showed similar potency in the human IL-6 assay ascompared to D56-05.

TABLE B9-1 Induction of IL-6 from Human B Cells by D56-05 (aka[(D56-01)- PEG₆]_(x)-FICOLL) Conjugates Produced with VariousD56-01:FICOLL Molar Ratios (x) as EC50 (mM) D56- D56-05 D56-05 D56-05D56-05 D56-05 D56-05 Donor # 01 x = 140 x = 24 x = 53 x = 82 x = 124 x =154 Do 1 0.056 0.021 0.025 0.020 0.020 0.025 0.007 Do 2 0.067 0.0160.020 0.020 0.015 0.020 0.016 Do 3 0.063 0.025 0.039 0.029 0.021 0.0180.020 Do 4 0.063 ND 0.030 0.016 0.016 0.019 0.035 Do 5 0.056 ND 0.0320.029 0.013 0.023 0.019 Ave 0.061 0.021 0.029 0.023 0.017 0.021 0.019 SD0.005 0.004 0.008 0.006 0.003 0.003 0.010 Count 5 3 5 5 5 5 5 SEM 0.0020.003 0.003 0.003 0.002 0.001 0.004 Mean 0.061 0.020 0.028 0.022 0.0170.021 0.017 ND = not determined; D56-05 with x = 140 is Pilot Lot 2 andwas used as a positive control in this experiment

Example B10 In Vitro Potency Evaluation of D56-05, D56-25, D56-26 andD56-27 (aka [(D56-01)-PEG_(n)]_(x)-FICOLL) Manufactured Using SM-PEG_(n)with n=6, 24, 45, and 70

The effect of varying the length (n) of the SM-PEG_(n) linker moleculein [(D56-01)-PEG_(n)]_(x)-FICOLL was tested by measuring potency of thein vitro biological response. The in vitro potency in human pDC-enrichedPBMC and B cells was determined as described in Example B1 for[(D56-01)-PEG_(n)]_(x)-FICOLL conjugates, D56-05, D56-25, D56-26 andD56-27, manufactured using SM-PEG_(n) with n=6, 24, 45 and 70,respectively, as described in Example S3 and Example S13. Results forthe human pDC-enriched PBMC IFN-α assay and the human B cell IL-6 assayare shown in Table B10-1 and Table B10-2, respectively.[(D56-01)-PEG_(n)]_(x)-FICOLL conjugates with longer PEG linkers showedslightly increased potency in the IFN-α assay and slightly reducedpotency in the IL-6 assay.

TABLE B10-1 Induction of IFN-α from Human pDC-enriched PBMC by[(D56-01)-PEG_(n)]_(x)-FICOLL Conjugates Produced with DifferentSM-PEG_(n) Linkers as EC50 (mM) (D56-01)- (D56-01)- (D56-01)- (D56-01)-(D56-01)- PEG₆- PEG₆- PEG₂₄- PEG₄₅- PEG₇₀- Donor # FICOLL^(a) FICOLLFICOLL FICOLL FICOLL Do 1 0.010 0.009 0.005 0.004 0.004 Do 2 0.012 0.0130.007 0.006 0.005 Do 3 0.007 0.006 0.004 0.003 0.004 Do 4 0.004 0.0040.003 0.002 0.003 Do 5 0.004 0.005 0.004 0.003 0.004 Do 6 0.007 0.0100.004 0.006 0.005 Ave 0.008 0.008 0.004 0.004 0.004 SD 0.003 0.003 0.0010.001 0.001 Count 6 6 6 6 6 SEM 0.001 0.001 0.001 0.001 0.000 Mean 0.0070.007 0.004 0.004 0.004 ^(a)Pilot lot 4.

TABLE B10-2 Induction of IL-6 from Human B Cells by [(D56-01)-PEG_(n)]_(x)-FICOLL Conjugates Produced with Various SM-PEG(n)Linkers as EC50 (mM) (D56-01)- (D56-01)- (D56-01)- (D56-01)- (D56-01)-PEG₆- PEG₆- PEG₂₄- PEG₄₅- PEG₇₀- Donor # FICOLL^(a) FICOLL FICOLL FICOLLFICOLL Do 7 0.019 0.003 0.004 0.007 0.007 Do 8 0.016 0.004 0.008 0.0080.006 Do 9 0.013 0.002 0.003 0.003 0.009 Do 10 0.014 0.002 0.002 0.0050.011 Do 11 0.016 0.003 0.005 0.006 0.007 Ave 0.016 0.003 0.005 0.0060.008 SD 0.002 0.001 0.002 0.002 0.002 Count 5 5 5 5 5 SEM 0.001 0.0000.001 0.001 0.001 Mean 0.016 0.003 0.004 0.005 0.008 ^(a)Pilot lot 4.

1. A branched chimeric compound of formula (I):[D-L¹-L²-(PEG)-L³]_(x)F  (I) wherein: D is a polynucleotide or a linearchimeric compound; L¹ is a first linker comprising an alkylthio group;L² is a second linker comprising a succinimide group; L³ is a thirdlinker comprising an amide group; PEG is of the formula —(OCH₂CH₂)_(n)—,where n is an integer from 2 to 80; x is an integer from 3 to 300; and Fis a branched copolymer of sucrose and epichlorohydrin having amolecular weight of about 100,000 to about 700,000 daltons and isconnected to L³ via an ether group, wherein the polynucleotide of Dcomprises the nucleotide sequence: 5′-TCGGCGC AACGTTC TCGGCGC-3′ (SEQ IDNO:1), wherein the polynucleotide is less than 50 nucleotides in length,and wherein one or more linkages between the nucleotides and between the3′-terminal nucleotide and L¹ are phosphorothioate ester linkages; andwherein the linear chimeric compound of D comprises three nucleic acidmoieties and two hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides, andwherein one or more linkages between the nucleotides, between thenucleotides and the HEG spacers and between the 3′-terminal nucleotideand L¹ are phosphorothioate ester linkages.
 2. The branched chimericcompound of claim 1, wherein L² is


3. The branched chimeric compound of claim 1, wherein L³ is:


4. The branched chimeric compound of claim 1, wherein n of the formula—(OCH₂CH₂)_(n)— is 6, 24, 45 or
 70. 5. The branched chimeric compound ofclaim 1, wherein F has a molecular weight of about 300,000 to about500,000 daltons.
 6. The branched chimeric compound of claim 1, wherein Dis the polynucleotide consisting of the nucleotide sequence 5′-TCGGCGCAACGTTC TCGGCGC-3′ (SEQ ID NO:1).
 7. The branched chimeric compound ofclaim 1, wherein D is the linear chimeric compound consisting of5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2).
 8. Thebranched chimeric compound of claim 1, wherein L¹ is —(CH₂)_(m)—S—,wherein m is an integer from 2 to
 9. 9. The branched chimeric compoundof claim 1, wherein x is from 20 to
 200. 10. The branched chimericcompound of claim 9, wherein x is from 90 to 150, n is 6 and m is 3 or6.
 11. The branched chimeric compound of claim 1, wherein all of thelinkages between the nucleotides, where present the linkages between thenucleotides and the HEG spacers, and the linkage between the 3′-terminalnucleotide and L¹ are phosphorothioate ester linkages. 12-17. (canceled)18. A linear chimeric compound comprising two nucleic acid moieties anda hexaethylene glycol (HEG) spacer as 5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′(SEQ ID NO:4), wherein the linear chimeric compound contains fewer than50 nucleotides, and wherein one or more linkages between the nucleotidesand between the nucleotides and the HEG spacer are phosphorothioateester linkages.
 19. A linear chimeric compound comprising three nucleicacid moieties and two hexaethylene glycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains fewer than 50 nucleotides, andwherein one or more linkages between the nucleotides and between thenucleotides and the HEG spacers are phosphorothioate ester linkages. 20.The linear chimeric compound of claim 19, wherein the linear chimericcompound consists of 5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′(SEQ ID NO:2).
 21. The linear chimeric compound of claim 19, wherein thenucleic acid moieties are 2′-deoxyribonucleotides.
 22. The linearchimeric compound of claim 19, wherein all of the linkages arephosphorothioate ester linkages.
 23. A pharmaceutical compositioncomprising (i) a pharmaceutically acceptable excipient, and (ii) thebranched chimeric compound of claim
 1. 24. The pharmaceuticalcomposition of claim 23, wherein the branched chimeric compound iscapable of stimulating cytokine production by mammalian leukocytes,comprising one or more of the group consisting of: stimulatingproduction of IFN-alpha by human peripheral blood mononuclear cells;stimulating production of IL-6 by human B lymphocytes; and stimulatingproduction of one or both of IL-12p40 and IL-6 by mouse splenocytes. 25.The pharmaceutical composition of claim 23, wherein the branchedchimeric compound is capable of stimulating proliferation of mammalian Blymphocytes.
 26. The pharmaceutical composition of claim 23, wherein thecomposition is a sterile solution.
 27. The pharmaceutical composition ofclaim 23, wherein the composition further comprises an antigen that isnot covalently-linked to the branched chimeric compound.
 28. Thepharmaceutical composition of claim 27, wherein the antigen is amicrobial antigen, an allergen or a tumor antigen.
 29. Thepharmaceutical composition of claim 23, wherein the composition isessentially endotoxin-free.
 30. A method of stimulating an immuneresponse in a mammalian subject, comprising administering to a mammaliansubject a pharmaceutical composition of claim 23 in an amount sufficientto stimulate an immune response in the mammalian subject.
 31. The methodof claim 30, wherein stimulating an immune response comprises one ormore of the group consisting of: stimulating IFN-alpha production;stimulating IL-6 production; stimulating B lymphocyte proliferation;stimulating interferon pathway-associated gene expression; stimulatingchemoattractant-associated gene expression; and stimulating plasmacytoiddendritic cell (pDC) maturation.
 32. The method of claim 30, whereinwhen the pharmaceutical composition further comprises an antigen,stimulating an immune response comprises inducing an antigen-specificantibody response, wherein titer of the antigen-specific antibodyresponse is higher when the antigen is administered in combination withthe branched chimeric compound than when the antigen is administeredwithout the branched chimeric compound.
 33. A method of inducing anantigen-specific antibody response in a mammalian subject, comprisingadministering to a mammalian subject the pharmaceutical composition ofclaim 27 in an amount sufficient to induce an antigen-specific antibodyresponse in the mammalian subject.
 34. A method of preventing aninfectious disease in a mammalian subject, comprising administering to amammalian subject a pharmaceutical composition of claim 23 in an amountsufficient to prevent an infectious disease in the mammalian subject.35. A method of ameliorating a symptom of an infectious disease in amammalian subject, comprising administering to a mammalian subject apharmaceutical composition of claim 23 in an amount sufficient toameliorate a symptom of an infectious disease in the mammalian subject.36. A method of ameliorating a symptom of an IgE-related disorder in amammalian subject, comprising administering to the mammalian subject apharmaceutical composition of claim 23 in an amount sufficient toameliorate a symptom of an IgE-related disorder in the mammaliansubject.
 37. A method of treating cancer in a mammalian subject,comprising administering to a mammalian subject a pharmaceuticalcomposition of claim 23 in an amount sufficient to treat cancer in themammalian subject.
 38. The method of claim 37, wherein treating cancercomprises shrinking size of a solid tumor.
 39. A method for preparing abranched chimeric compound of formula (I):[D-L¹-L²-(PEG)-L³]_(x)-F  (I) wherein: D is a polynucleotide or a linearchimeric compound; L¹ is a first linker comprising an alkylthio group;L² is a second linker comprising a succinimide group; L³ is a thirdlinker comprising an amide group; PEG is a polyethylene glycol; x is aninteger from 3 to 300; and F is a branched copolymer of sucrose andepichlorohydrin having a molecular weight of about 100,000 to about700,000 daltons and is connected to L³ via an ether group, wherein thepolynucleotide comprises the nucleotide sequence: 5′-TCGGCGC AACGTTCTCGGCGC-3′ (SEQ ID NO:1), wherein the polynucleotide is less than 50nucleotides in length, and wherein one or more linkages between thenucleotides and between the 3′-terminal nucleotide and L¹ arephosphorothioate ester linkages, and wherein the linear chimericcompound comprises three nucleic acid moieties and two hexaethyleneglycol (HEG) spacers as5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2), whereinthe linear chimeric compound contains less than 50 nucleotides, andwherein one or more linkages between the nucleotides, between thenucleotides and the HEG spacers and between the 3′-terminal nucleotideand L¹ are phosphorothioate ester linkages, wherein the methodcomprises: reacting a compound of the formula D-L^(1a)-SH, where D is asdefined for formula (I) and L^(1a) is (CH₂)_(m) where m is an integerfrom 2 to 9, with a compound of formula (II):[L^(2a)-(PEG)-L³]_(y)-F  (II) wherein L³, PEG and F are as defined forformula (I); L^(2a) is

and y is an integer from 3 to
 350. 40. The method according to claim 39,further comprising reacting a compound of the formulaD-L^(1a)-SS-L^(1a)-OH with a reducing agent to produce the compound ofthe formula D-L^(1a)-SH.
 41. The method according to claim 39, furthercomprising reacting a compound of the formula (III):[NH₂CH₂CH₂NHC(O)CH₂]_(z)—F  (III) wherein F is as defined for formula(I) and z is an integer from 3 to 400, with a compound of the formulaL^(2a)-(PEG)-L^(3a)-Lv, where L^(2a) and PEG are as defined for formula(II); L^(3a) is —NHC(O)CH₂CH₂C(O)— or —C(O)—; and Lv is a leaving group,to form the compound of the formula (II).
 42. The method according toclaim 41, wherein Lv is (2,5-dioxopyrrolidin-1-yl)oxy.
 43. The methodaccording to claim 39, wherein D is5′-TCGGCGC-3′-HEG-5′-AACGTTC-3′-HEG-5′-TCGGCGC-3′ (SEQ ID NO:2).
 44. Themethod according to claim 39, wherein D is 5′-TCGGCGC AACGTTC TCGGCGC-3′(SEQ ID NO:1).